Installation problem V1.40

From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From k.byriel@imb.uq.edu.au Wed Sep 4 07:39:42 2002 From: k.byriel@imb.uq.edu.au (Karl A. Byriel) Date: Wed, 04 Sep 2002 16:39:42 +1000 Subject: [sharp-discuss] Installation problem V1.40 Message-ID: > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3114002383_27033131 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, We are having problems with the httpd part of the installation. We have a Redhat 7.2 system and are using the httpd that is available with the helpers. We can get the web server running and all other parts of the installation, but we only get a blank screen in the web browser. The httpd logs indicate users are connecting, and the users can view the page source and see: There are no error logs being generated. Can anyone help? Thanks, Karl Karl A. Byriel Structural Biology Division Institute for Molecular Bioscience The University of Queensland Qld 4072 Australia Phone: 61-7-33654941 Fax: 61-7-33651990 Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au --B_3114002383_27033131 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable Installation problem V1.40 Hi,

We are having problems with the httpd part of the installation. We have a R= edhat 7.2 system and are using the httpd that is available with the helpers.= We can get the web server running and all other parts of the installa= tion, but we only get a blank screen in the web browser. The httpd log= s indicate users are connecting, and the users can view the page source and = see:

There are no error logs being generated. &= nbsp;Can anyone help?

Thanks,

Karl

Karl A. Byriel
Structural Biology Division
Institute for Molecular Bioscience
The University of Queensland Qld 4072 Australia
Phone: 61-7-33654941 Fax: 61-7-33651990
Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au

--B_3114002383_27033131-- From vonrhein@globalphasing.com Wed Sep 4 08:28:34 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 08:28:34 +0100 Subject: [sharp-discuss] Installation problem V1.40 In-Reply-To: References: Message-ID: <20020904072834.GA32246@galois.globalphasing.com> Dear Karl, difficult to tell. Here are some possibilities/remarks: - is the user running the httpd in a different UNIX group to the ordinary SHARP/autoSHARP user? Remember, this httpd-running user has to be able to cd $BDG_home/users/karl/sharpfiles and then read/write in all subdirectories (datafiles, cardfiles and the various logfiles() - did you run all necessary installation scripts: 1. installSHARP 2. newmachine 3. newuser and has the user created by step 3 run the 'useSHARP' command? (see http://www.globalphasing.com/sharp/installation/index.html#quick) - try running the checking script, described in http://www.globalphasing.com/sharp/installation/index.html#trouble - have a look at the log files in $BDG_home/sushi/logs/error_log: any meaningful message? Hope that gives some help ... Cheers Clemens PS: please subscribe to sharp-discuss before sending emails to the list - otherwise they could be delayed. On Wed, Sep 04, 2002 at 04:39:42PM +1000, Karl A. Byriel wrote: > Hi, > > We are having problems with the httpd part of the installation. We have a > Redhat 7.2 system and are using the httpd that is available with the > helpers. We can get the web server running and all other parts of the > installation, but we only get a blank screen in the web browser. The httpd > logs indicate users are connecting, and the users can view the page source > and see: > > > > There are no error logs being generated. Can anyone help? > > Thanks, > > Karl > > Karl A. Byriel > Structural Biology Division > Institute for Molecular Bioscience > The University of Queensland Qld 4072 Australia > Phone: 61-7-33654941 Fax: 61-7-33651990 > Mobile: 0400 209 186 HTTP://www.imb.uq.edu.au > > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From khkim@korea.ac.kr Wed Sep 4 13:30:05 2002 From: khkim@korea.ac.kr (=?ks_c_5601-1987?B?seiw5sf2?=) Date: Wed, 4 Sep 2002 21:30:05 +0900 Subject: [sharp-discuss] solomon error Message-ID: <007c01c2540e$cc9f1c10$bf9d98a3@xtal5> This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 SSBoYXZlIHByb2JsZW1zIGR1cmluZyBzb2xvbW9uLCB3aXRoIGEgbWVzc2FnZSAiIEZhdGFsIGRp c2FncmVlbWVudCBiZXR3ZWVuIGlucHV0IGluZm8gYW5kIG1hcCBoZWFkZXIiLiBJdCBzZWVtcyB0 aGUgbWFwIGdlbmVyYXRlZCBieSBmZnQgb3IgbWFwbWFzayBpcyBsaW1pdGVkIHRvIGFzdSBhbmQg c2ZhbGwgY29tcGxhaW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLg0KDQpJIGNoZWNrZWQgc29sb21v bi5zaCB3aGVyZSBGRlR4eXpsaW0gaXMgYXNzaWduZWQgd2l0aCBhc3V4eXpsaW0uIENoYW5naW5n IHRlIGFzdXh5emxpbSB0byBjZWxseHl6bGltIGRpZCBub3QgZ2l2ZSBtZSBhbiBlcnJvci4gSSB3 b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuICBUaGFua3MuDQoNCksuSC4NCg== ------=_NextPart_000_0079_01C2545A.3C73B140 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI2MDAuMCIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwvSEVB RD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgaGF2ZSBwcm9i bGVtcyBkdXJpbmcgc29sb21vbiwgd2l0aCBhIG1lc3NhZ2UgPC9GT05UPjxGT05UIA0Kc2l6ZT0y PiIgRmF0YWwmbmJzcDtkaXNhZ3JlZW1lbnQgYmV0d2VlbiBpbnB1dCBpbmZvIGFuZCBtYXAgDQpo ZWFkZXIiLjwvRk9OVD4mbmJzcDs8Rk9OVCBzaXplPTI+SXQgc2VlbXMgdGhlIG1hcCBnZW5lcmF0 ZWQgYnkgZmZ0IG9yIG1hcG1hc2sgDQppcyBsaW1pdGVkIHRvIGFzdSBhbmQgc2ZhbGwgY29tcGxh aW5zIGFib3V0IGl0IChTcGcgUDYzMjIpLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkkgY2hlY2tlZCBzb2xvbW9u LnNoIHdoZXJlIEZGVHh5emxpbSANCmlzJm5ic3A7YXNzaWduZWQmbmJzcDt3aXRoIGFzdXh5emxp bS4gQ2hhbmdpbmcmbmJzcDt0ZSBhc3V4eXpsaW0gdG8gY2VsbHh5emxpbSANCmRpZCBub3QgZ2l2 ZSBtZSBhbiBlcnJvci4gSSB3b25kZXIgd2hldGhlciB0aGlzIGlzIGNvcnJlY3QuIA0KJm5ic3A7 VGhhbmtzLjwvRk9OVD48L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9 Mj5LLkguPC9GT05UPjwvRElWPjwvQk9EWT48L0hUTUw+DQo= ------=_NextPart_000_0079_01C2545A.3C73B140-- From vonrhein@globalphasing.com Wed Sep 4 14:01:01 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Wed, 4 Sep 2002 14:01:01 +0100 Subject: [sharp-discuss] solomon error Message-ID: <20020904130101.GH32246@galois.globalphasing.com> Aaahhh ... one of my favourites: asymmetric unit conventions! One important bit: are you running the latest version of Sushi (3.0.9) and CCP4 (4.2.1)? And what does the header of you solo_XX.Xpc.log.html file say about asymmetric units (if anything at all). The point is, that finding the asymmetric units that various programs are writing and/or expecting is a bit tricky - and it's possible that there is a problem for your particular spacegroup. Instead of changing the code in solomon.sh you can also edit $BDG_home/database/lists/symm.dat, search for a line starting with P6322 and change fields 6, 8 and 10 (delimited by a colon ":") to "0. 1. 0. 1. 0. 1.". This will tell all SHARP/autoSHARP programs to use the whole unit cell as 'asymmetric unit'. For the next SHARP/autoSHARP release I revisited this list of spacegroup specific definitions - hopefully it will be completely up-to-date for the latest CCP4 4.2.1 (and above) release. Hope that helps. Cheers Clemens PS: could you please subscribe to sharp-discuss mailing list before posting there? On Wed, Sep 04, 2002 at 09:30:05PM +0900, 김경현 wrote: > I have problems during solomon, with a message " Fatal disagreement between input info and map header". It seems the map generated by fft or mapmask is limited to asu and sfall complains about it (Spg P6322). > > I checked solomon.sh where FFTxyzlim is assigned with asuxyzlim. Changing te asuxyzlim to cellxyzlim did not give me an error. I wonder whether this is correct. Thanks. > > K.H. -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From taylor@bioc09.v19.uthscsa.edu Thu Sep 12 22:43:30 2002 From: taylor@bioc09.v19.uthscsa.edu (Alex Taylor) Date: Thu, 12 Sep 2002 16:43:30 -0500 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit Message-ID: <3D810A82.5040507@biochem.uthscsa.edu> Dear SHARP Users, I am running into trouble running AutoSHARP using MAD data. I can howver successfully solve a SAD problem. The error occurs after scaling the first two wavelengths as listed below using the IF3-C MAD tutorial for example: 2.2 second analysis run (exclusion of outliers) (details) (analysis of scaling) (analysis of scaling) NOTE : Scale factor = 0.999 NOTE : Gradients should be > 1.0 and intercept = 0 Gradient [probability > 0.9] (centric) = 0.966 (acentric) = 0.765 Intercept [probability > 0.9] (centric) = -0.068 (acentric) = -0.019 R-factor (F) = 0.032 R-factor (I) = 0.040 R-factor (weighted) = 0.044 /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot create unique file name in "/tmp". awk: Cannot divide by zero. The input line number is 1. The source line number is 2. awk: Cannot divide by zero. The input line number is 1. The source line number is 2. /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: argument expected I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced these 'cannot create unique file name in "/tmp"' or awk problems and solved them? I tried assigning different tmp directories for sharp, ccp4, and binsort files and nothing worked so far. Thanks, Alex -- Alex Taylor, Ph.D. Department of Biochemistry University of Texas Health Science Center at San Antonio From vonrhein@globalphasing.com Fri Sep 13 07:59:07 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Fri, 13 Sep 2002 07:59:07 +0100 Subject: [sharp-discuss] AutoSHARP crashing after Scaleit In-Reply-To: <3D810A82.5040507@biochem.uthscsa.edu> References: <3D810A82.5040507@biochem.uthscsa.edu> Message-ID: <20020913065906.GB5666@galois.globalphasing.com> Dear Alex, I'm afraid this is a feature/bug (?) in Tru64 Unix. I _think_ it has to do with the way the Bourne executes something like #!/bin/sh f=FP s=SIGFP scaleit hklin my.mtz < Dear SHARP Users, > > I am running into trouble running AutoSHARP using MAD data. I can > howver successfully solve a SAD problem. The error occurs after scaling > the first two wavelengths as listed below using the IF3-C MAD tutorial > for example: > > 2.2 second analysis run (exclusion of outliers) > (details) (analysis of scaling) (analysis of scaling) > > NOTE : Scale factor = 0.999 > > NOTE : Gradients should be > 1.0 and intercept = 0 > > Gradient [probability > 0.9] (centric) = 0.966 > (acentric) = 0.765 > Intercept [probability > 0.9] (centric) = -0.068 > (acentric) = -0.019 > > R-factor (F) = 0.032 > R-factor (I) = 0.040 > R-factor (weighted) = 0.044 > > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: cannot > create unique file name in "/tmp". awk: Cannot divide by zero. The input > line number is 1. The source line number is 2. awk: Cannot divide by > zero. The input line number is 1. The source line number is 2. > /usr/progs/osf/sharp_090802/bin/sharp/autoSHARP/scaleit.sh: test: > argument expected > > I am running the latest SHARP and SUSHI on an Alpha Tru64 5.1A system > with the CCP4 4.2.1 binaries provided by CCP4. Has anyone experienced > these 'cannot create unique file name in "/tmp"' or awk problems and > solved them? I tried assigning different tmp directories for sharp, > ccp4, and binsort files and nothing worked so far. > > Thanks, > > Alex > > -- > Alex Taylor, Ph.D. > Department of Biochemistry > University of Texas Health Science Center at San Antonio > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From phubbard@post.its.mcw.edu Fri Sep 20 18:55:45 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Fri, 20 Sep 2002 12:55:45 -0500 (CDT) Subject: [sharp-discuss] wARP dummy atoms and SHARP/SOLOMON Message-ID: <6469.141.106.40.31.1032544545.squirrel@post.its.mcw.edu> Hi all, This may not be such a smart idea (hence this e-mail), but has anyone ever tried using the dummy atoms produced by wARP as a partial structure for SHARP/SOLOMON? Thanks AGS From phubbard@post.its.mcw.edu Tue Sep 24 15:39:39 2002 From: phubbard@post.its.mcw.edu (phubbard@post.its.mcw.edu) Date: Tue, 24 Sep 2002 09:39:39 -0500 (CDT) Subject: [sharp-discuss] SOLVE Scaled Data for SHARP Message-ID: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Hello, I have managed to phase really well in SHARP using just SAD data (SOLVE did a reasonable job), and I have managed to phase even better with SOLVE when I combine in-house SAD data with synchrotron MAD data. I have a feeling I can phase better still if I use SHARP with the MAD and SAD data; however, it keeps getting lost during refinement. I scale the MAD data (3A) to the in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: C-1 X-1 (MAD DATA) W-1 B-1 W-2 B-2 W-3 B-3 X-2 (SAD DATA) W-1 B-1 Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful of any other suggestions. Thanks AGS SHARP SAD OUTPUT **************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 Y 0.1646 0.0000 0.1646 0.0005 Z 0.1359 0.0000 0.1359 0.0006 G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 Y 0.1617 0.0000 0.1617 0.0004 Z 0.1633 0.0000 0.1632 0.0004 G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 Y 0.1588 0.0000 0.1588 0.0003 Z 0.1482 0.0000 0.1482 0.0004 G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 Y 0.1398 0.0000 0.1398 0.0004 Z 0.1477 0.0000 0.1477 0.0004 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 HAT_B 67.9279 -0.1567 67.7713 7.2571 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 HAT_B 46.0304 -0.1130 45.9174 3.9446 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 HAT_B 51.5399 0.0029 51.5429 3.7114 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 HAT_B 36.1583 -0.1484 36.0099 3.0819 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 NANO_CLOC 0.0180 0.0012 0.0191 0.0017 SHARP MAD + SAD OUTPUT ********************** Cpd Cry Wvl Bat Parameter Old Shift New SD G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 Y 0.1617 -0.0006 0.1611 0.0000 Z 0.1242 0.0009 0.1250 0.0000 G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 Y 0.1684 -0.0014 0.1670 0.0000 Z 0.1630 0.0014 0.1644 0.0000 G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 Y 0.1591 0.0000 0.1591 0.0000 Z 0.1530 -0.0001 0.1529 0.0000 G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 Y 0.1345 0.0002 0.1347 0.0000 Z 0.1532 0.0001 0.1532 0.0000 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 HAT_B 29.8155 -3.4500 26.3654 0.0267 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 HAT_B 28.6382 10.4000 39.0382 0.0712 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 HAT_B 19.7436 -18.5356 1.2079 0.1247 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 | | SCAL_B -0.3746 0.8976 0.5230 0.0168 | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 | SCAL_B -2.5194 1.4793 -1.0402 0.0334 | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 HAT_B 27.0277 11.5754 38.6032 0.0800 \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 HAT_B 32.5326 29.3245 61.8572 0.1972 \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 HAT_B 30.9187 -6.8453 24.0734 0.0471 \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 HAT_B 29.6765 -6.4903 23.1862 0.0458 \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 SCAL_B 2.0742 -0.9987 1.0756 0.0098 NISO_BGLO 0.0709 0.1067 0.1776 0.0007 NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 NANO_CLOC 2.6589 0.5016 3.1606 0.0299 From moiseeva@usc.edu Thu Sep 26 04:33:09 2002 From: moiseeva@usc.edu (natalia moiseeva) Date: Wed, 25 Sep 2002 20:33:09 -0700 Subject: [sharp-discuss] ARP/wARP 6.0 running error Message-ID: Hello, I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: running arpwarp.sh..... step 2.3 building initial model error: program terminated in ARP_wARP, see *.log the information from log file: ############################################################################### ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### ############ Copyright 1998 European Molecular Biology Laboratory ############# ############################################################################### User: Unknown Run date: 25.09.02 Run time:19:29:54 0.00 CPU 0 Elapsed Data line -- MODE MIRBUILD Required keywords: FILES CCP4 file_names CELL cell parameters SYMM spacegroup RESOLUTION resmin resmax MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM END (must be the last keyword) Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 .pdb Data line -- SYMM 19 Space group number 19 P212121 No of symmetry operators 4 1 symmetry matrix (identity matrix) and translation vector: 1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 0.000 2 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 0.500 3 symmetry matrix (2-fold rotation) and translation vector: -1.000 0.000 0.000 0.000 0.000 1.000 0.000 0.500 0.000 0.000 -1.000 0.500 4 symmetry matrix (2-fold rotation) and translation vector: 1.000 0.000 0.000 0.500 0.000 -1.000 0.000 0.500 0.000 0.000 -1.000 0.000 Asymmetric unit limits 1 / 1 1 / 1 1 / 4 Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 Data line -- RESOLUTION 21.818 0.95 Data line -- MIRBUILD ATOMS 499 MODELS 1 This Data Card is not understood: MIRBUILD ATOMS 499 MODELS 1 Missing keyword RESN Expected format: MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM ***** ERROR ***** Could you recommend me what to do in this case? Sincerely, Natalia Moiseeva From vonrhein@globalphasing.com Thu Sep 26 11:35:09 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 11:35:09 +0100 Subject: [sharp-discuss] SOLVE Scaled Data for SHARP In-Reply-To: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> References: <9222.141.106.40.31.1032878379.squirrel@post.its.mcw.edu> Message-ID: <20020926103509.GB17851@galois.globalphasing.com> Hi, difficult to tell. I could think of several reasons: - scaling (as you mentioned): if your MAD and SAD data contain the same scatterers I would assume that SCALEIT might do a better job. Remember: FHSCAL assumes you scale derivative to native, where the derivative has additional (heavy) atom contribution. - scaling (2): by scaling the 3 MAD to the SAD your previous scaling between the MAD wavelengths get lost. I would rather scale the SAD to the best MAD wavelegths. This way you don't change a lot compared to your previous SHAR run. - scaling (3): you could also just skip any external scaling and add the SAD wavelength to the end_*.sin SHARP run: by specifying ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with reasonable scales and you can refine them. - indexing? I guess there can't be a problem that the datasets are indexed differently? - your coordinates are quite different for your MAD+SAD run: did you start with the end_*.sin file from the best MAD run and just added a new crystal? If you could give a bit more information about data quality, scatterer and send me some SIN files I might be able to give a few more suggestions. Cheers Clemens On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote: > Hello, > > I have managed to phase really well in SHARP using just SAD data (SOLVE did > a reasonable job), and I have managed to phase even better with SOLVE when I > combine in-house SAD data with synchrotron MAD data. I have a feeling I can > phase better still if I use SHARP with the MAD and SAD data; however, it > keeps getting lost during refinement. I scale the MAD data (3A) to the > in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following: > > C-1 > X-1 (MAD DATA) > W-1 > B-1 > W-2 > B-2 > W-3 > B-3 > X-2 (SAD DATA) > W-1 > B-1 > > Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried > converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful > of any other suggestions. > > Thanks > > AGS > > SHARP SAD OUTPUT > **************** Cpd Cry Wvl Bat Parameter Old Shift > New SD > > G-SITE-001 X 0.1734 0.0000 0.1733 0.0009 > Y 0.1646 0.0000 0.1646 0.0005 > Z 0.1359 0.0000 0.1359 0.0006 > G-SITE-002 X 0.1781 0.0000 0.1782 0.0008 > Y 0.1617 0.0000 0.1617 0.0004 > Z 0.1633 0.0000 0.1632 0.0004 > G-SITE-003 X 0.1410 0.0000 0.1410 0.0007 > Y 0.1588 0.0000 0.1588 0.0003 > Z 0.1482 0.0000 0.1482 0.0004 > G-SITE-004 X 0.1706 0.0000 0.1705 0.0005 > Y 0.1398 0.0000 0.1398 0.0004 > Z 0.1477 0.0000 0.1477 0.0004 > 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081 > HAT_B 67.9279 -0.1567 67.7713 7.2571 > 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901 > HAT_B 46.0304 -0.1130 45.9174 3.9446 > 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901 > HAT_B 51.5399 0.0029 51.5429 3.7114 > 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698 > HAT_B 36.1583 -0.1484 36.0099 3.0819 > 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815 > NANO_CLOC 0.0180 0.0012 0.0191 0.0017 > > SHARP MAD + SAD OUTPUT > ********************** > > Cpd Cry Wvl Bat Parameter Old Shift New SD > > G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000 > Y 0.1617 -0.0006 0.1611 0.0000 > Z 0.1242 0.0009 0.1250 0.0000 > G-SITE-002 X 0.1974 0.0015 0.1989 0.0000 > Y 0.1684 -0.0014 0.1670 0.0000 > Z 0.1630 0.0014 0.1644 0.0000 > G-SITE-003 X 0.1457 0.0002 0.1459 0.0000 > Y 0.1591 0.0000 0.1591 0.0000 > Z 0.1530 -0.0001 0.1529 0.0000 > G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000 > Y 0.1345 0.0002 0.1347 0.0000 > Z 0.1532 0.0001 0.1532 0.0000 > 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016 > HAT_B 29.8155 -3.4500 26.3654 0.0267 > 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020 > 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028 > HAT_B 28.6382 10.4000 39.0382 0.0712 > 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037 > HAT_B 19.7436 -18.5356 1.2079 0.1247 > 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784 > | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158 > | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002 > | | SCAL_B -0.3746 0.8976 0.5230 0.0168 > | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982 > | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004 > | SCAL_B -2.5194 1.4793 -1.0402 0.0334 > | NANO_CLOC 5.2742 2.4323 7.7064 0.0831 > \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007 > HAT_B 27.0277 11.5754 38.6032 0.0800 > \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008 > HAT_B 32.5326 29.3245 61.8572 0.1972 > \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018 > HAT_B 30.9187 -6.8453 24.0734 0.0471 > \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016 > HAT_B 29.6765 -6.4903 23.1862 0.0458 > \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001 > SCAL_B 2.0742 -0.9987 1.0756 0.0098 > NISO_BGLO 0.0709 0.1067 0.1776 0.0007 > NISO_CLOC 0.0009 -0.0009 0.0000 0.0000 > NANO_CLOC 2.6589 0.5016 3.1606 0.0299 > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) *************************************************************** From vonrhein@globalphasing.com Thu Sep 26 12:00:49 2002 From: vonrhein@globalphasing.com (Clemens Vonrhein) Date: Thu, 26 Sep 2002 12:00:49 +0100 Subject: [sharp-discuss] ARP/wARP 6.0 running error In-Reply-To: References: Message-ID: <20020926110049.GE17851@galois.globalphasing.com> Dear Natalia, the latest ARP/wARP is not fully supported by the current Sushi version (3.0.9). I just finished upgrading the interface between SHARP and the latest ARP/wARP (works very nicely). So I expect a new Sushi release within the next few days. In the meantime: if you still have ARP/wARP 5.1 installed please configure SHARP to use this (using the $BDG_home/adm/bin/arpwarp-setup script). Or use the new ARP/wARP through the CCP4i interface ... Cheers Clemens On Wed, Sep 25, 2002 at 08:33:09PM -0700, natalia moiseeva wrote: > Hello, > > I have a problem of running ARP/wARP 6.0 with current SHARP version. After submitting a job for automated model building I got the following error message: > running arpwarp.sh..... > step 2.3 building initial model > error: program terminated in ARP_wARP, see *.log > the information from log file: > > ############################################################################### > ### ARP/wARP Program Suite: ARP Ver. 6.0 20 Jun 2002 V.Lamzin & A.Perrakis ### > ############ Copyright 1998 European Molecular Biology Laboratory ############# > ############################################################################### > > User: Unknown Run date: 25.09.02 Run time:19:29:54 > > 0.00 CPU 0 Elapsed > Data line -- MODE MIRBUILD > > Required keywords: > FILES CCP4 file_names > CELL cell parameters > SYMM spacegroup > RESOLUTION resmin resmax > MIRBUILD ATOMS number MODELS number RESNAM WAT/DUM > > > END (must be the last keyword) > > Data line -- FILES CCP4 MAPFIND ./files/mapmask.map XYZOUT1 ./files/arp_warp_cycle0 > .pdb > Data line -- SYMM 19 > > Space group number 19 P212121 > No of symmetry operators 4 > > 1 symmetry matrix (identity matrix) and translation vector: > 1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.000 > 0.000 0.000 1.000 0.000 > > 2 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.000 > 0.000 0.000 1.000 0.500 > > 3 symmetry matrix (2-fold rotation) and translation vector: > -1.000 0.000 0.000 0.000 > 0.000 1.000 0.000 0.500 > 0.000 0.000 -1.000 0.500 > > 4 symmetry matrix (2-fold rotation) and translation vector: > 1.000 0.000 0.000 0.500 > 0.000 -1.000 0.000 0.500 > 0.000 0.000 -1.000 0.000 > > Asymmetric unit limits 1 / 1 1 / 1 1 / 4 > > > Data line -- CELL 34.0150 34.3880 43.6350 90.0000 90.0000 90.0000 > Data line -- RESOLUTION 21.818 0.95 > Data line -- MIRBUILD ATOMS 499 MODELS 1 > > This Data Card is not understood: > > MIRBUILD ATOMS 499 MODELS 1 > > Missing keyword RESN > > Expected format: > > MIRBUILD ATOMS number MODELS number RESNUM WAT/DUM > > ***** ERROR ***** > > > Could you recommend me what to do in this case? > > Sincerely, > > Natalia Moiseeva > > > > > > _______________________________________________ > sharp-discuss mailing list > sharp-discuss@globalphasing.com > http://www.globalphasing.com/mailman/listinfo/sharp-discuss -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein@GlobalPhasing.com * * Global Phasing Ltd. * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************