From tea.pavkov@uni-graz.at Wed Jul 2 08:54:30 2003
From: tea.pavkov@uni-graz.at (Tea Pavkov)
Date: Wed, 2 Jul 2003 09:54:30 +0200
Subject: [sharp-discuss] labels
Message-ID: <006901c3406f$2b4ba0b0$0e2c328f@kfunigraz.ac.at>
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Hi all!
I tried to run SIRAS in SHARP, and I input native as compound 1, and =
derivative as compaund 2. Before I merged the 2 mtz files of native and =
derivative in one, so I have F, SIGF of native and F, SIGF, DANO, SANO =
and ISYM for derivative. So, for the first compound I only define F and =
SIGF for native. And when I run SHARP I get this errormessage. Can I =
leave "none" for the rest 3 colums or is that a problem?
Thank you
Tea
-------------------------------------------------------------------------=
-------------------------
Section 1 : INITIAL ESTIMATION OF PARAMETERS
*** Warning
From LRASSN : Program Label DANOw1 was not assigned
=20
=20
*** Warning
From LRASSN : Program Label SANOw1 was not assigned
=20
=20
*** Warning
From LRASSN : Program Label ISYMw1 was not assigned
=20
sharp: Error in label assignments
-------------------------------------------------------------------------=
------------------------------------------------
Mag. Pavkov Tea
K.F-Uni Graz, Institute for Chemistry
Structural Biology
Heinrichstrasse 28
8010 Graz, AT
Tel: +43 316 380 5414
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Hi all!
I tried to run SIRAS in SHARP, and I =
input native=20
as compound 1, and derivative as compaund 2. Before I merged the 2 mtz =
files of=20
native and derivative in one, so I have F, SIGF of native and F, SIGF, =
DANO,=20
SANO and ISYM for derivative. So, for the first compound I =
only define F=20
and SIGF for native. And when I run SHARP I get this errormessage. Can I =
leave=20
"none" for the rest 3 colums or is that a problem?
Thank you
Tea
----------------------------------------------------------------=
----------------------------------
Section =
1 :=20
INITIAL ESTIMATION OF PARAMETERS
*** Warning
From LRASSN : Program Label =
DANOw1 was=20
not assigned
*** =
Warning
From LRASSN=20
: Program Label SANOw1 was not =
assigned
*** =20
Warning
From LRASSN : Program Label ISYMw1 was not=20
assigned
sharp: Error in label=20
assignments
----------------------------------------------------------=
---------------------------------------------------------------
Mag. Pavkov Tea
K.F-Uni Graz, Institute for Chemistry
Structural Biology
Heinrichstrasse 28
8010 Graz, AT
Tel: +43 316 380 5414
------=_NextPart_000_0066_01C3407F.EECAFAD0--
From vonrhein@globalphasing.com Wed Jul 2 09:22:47 2003
From: vonrhein@globalphasing.com (Clemens Vonrhein)
Date: Wed, 2 Jul 2003 09:22:47 +0100
Subject: [sharp-discuss] labels
In-Reply-To: <006901c3406f$2b4ba0b0$0e2c328f@kfunigraz.ac.at>
References: <006901c3406f$2b4ba0b0$0e2c328f@kfunigraz.ac.at>
Message-ID: <20030702082247.GF23490@galois.globalphasing.com>
Dear Tea,
could you send the check_input.asc file please?
Is it possible that you started SHARP based on an existing SIN file
(that used a MTZ file with column names DANOw1, SANOw1 and ISYMw1)?
You then changed to using a different MTZ files (with different column
names DANO, SANO and ISYM)?
I guess the SIN file has a line like
COLUMN .... DANO=DANOw1 SANO=SANOw1 ISYM=ISYMw1
(which is wrong and should be DANO=DANO SANO=SANO ISYM=ISYM).
It is possible that the SIN file editor didn't pick up the changes of
column names: try going to the batch level of your native and
derivative and re-select the column names (which triggers a JavaScript
function to re-set the value of various variables).
It is always a bit tricky when you start SHARP based on a previous run
AND change the MTZ file. If you do that you need to go to all BATCH
levels and re-select the column names (even if they show up
correctly). ... it's a JavaScript 'feature' but I won't get into
details ...
Also: if you have two MTZ files
native : F SIGF
derivative: F SIGF DANO SANO ISYM
you can't just combine them using e.g. mtzutils (UNIQU keyword)! This
will leave you with a single column F and SIGF (which might even be a
combination of native and derivative). The way to do it is:
cad hklin1 nat.mtz hklin2 der.mtz hklout nat+der.data.mtz < this will make sure you have unique column names for each dataset.
Cheers
Clemens
On Wed, Jul 02, 2003 at 09:54:30AM +0200, Tea Pavkov wrote:
> Hi all!
> I tried to run SIRAS in SHARP, and I input native as compound 1, and derivative as compaund 2. Before I merged the 2 mtz files of native and derivative in one, so I have F, SIGF of native and F, SIGF, DANO, SANO and ISYM for derivative. So, for the first compound I only define F and SIGF for native. And when I run SHARP I get this errormessage. Can I leave "none" for the rest 3 colums or is that a problem?
>
> Thank you
>
> Tea
>
> --------------------------------------------------------------------------------------------------
> Section 1 : INITIAL ESTIMATION OF PARAMETERS
>
>
> *** Warning
> From LRASSN : Program Label DANOw1 was not assigned
>
>
> *** Warning
> From LRASSN : Program Label SANOw1 was not assigned
>
>
> *** Warning
> From LRASSN : Program Label ISYMw1 was not assigned
>
> sharp: Error in label assignments
> -------------------------------------------------------------------------------------------------------------------------
> Mag. Pavkov Tea
> K.F-Uni Graz, Institute for Chemistry
> Structural Biology
> Heinrichstrasse 28
> 8010 Graz, AT
> Tel: +43 316 380 5414
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT 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 gdbowman@uclink.berkeley.edu Thu Jul 17 01:42:35 2003
From: gdbowman@uclink.berkeley.edu (Gregory D. Bowman)
Date: Wed, 16 Jul 2003 17:42:35 -0700
Subject: [sharp-discuss] very low B-factors
Message-ID: <3F3E4F1B@bearmail.berkeley.edu>
Hello -
I am working with a 2-wavelength MAD dataset to about 3.2A resolution. From a
related crystal, I know the 17 Se sites pretty confidently, and these sites
seem to refine OK in SOLVE for the dataset I am having trouble with (so I am
pretty sure the sites are all real). With SHARP, the B-factor of one site
refines to 1.0. If I do not refine occupancies, the B-factor still dips pretty
low in the first cycle (B=2.5) but manages to recover somewhat by the final
cycle (B=56.7), though it is still relatively low for this resolution. Is it
the case that I simply do not have enough information to refine these
parameters at this resolution? Some of the logfile is below.
Thanks for any advice.
Greg
==============================
NOTE - site 6 is the offender. I apologise if the formatting does not carry
though in the email.
-------------------------------------------------------
refining both B and occupancies:
--------------------------------
First cycle of refining B/occupancies: Everything seems OK
001__G-SITE-001 HAT_OCC 1.1969 0.5500 1.7469
HAT_B 149.2960 -1.6175 147.6785
001__G-SITE-002 HAT_OCC 1.5708 0.7393 2.3100
HAT_B 155.8439 -1.5838 154.2601
001__G-SITE-003 HAT_OCC 1.5014 0.6834 2.1847
HAT_B 186.3591 -1.2411 185.1180
001__G-SITE-004 HAT_OCC 1.4379 0.6495 2.0874
HAT_B 199.2562 -1.3835 197.8728
001__G-SITE-005 HAT_OCC 1.8110 0.8303 2.6413
HAT_B 213.9898 -0.5395 213.4502
001__G-SITE-006 HAT_OCC 1.6478 0.7564 2.4041
HAT_B 155.2214 -1.8708 153.3506
001__G-SITE-007 HAT_OCC 1.1981 0.5572 1.7553
HAT_B 174.7769 -1.0286 173.7482
001__G-SITE-008 HAT_OCC 1.3638 0.6294 1.9932
HAT_B 185.8664 -0.9468 184.9196
001__G-SITE-009 HAT_OCC 1.6190 0.7405 2.3595
HAT_B 193.9789 -1.0006 192.9783
001__G-SITE-010 HAT_OCC 1.4603 0.6834 2.1437
HAT_B 200.6610 -0.5527 200.1083
001__G-SITE-011 HAT_OCC 1.4920 0.6880 2.1800
HAT_B 168.2568 -1.9167 166.3402
001__G-SITE-012 HAT_OCC 1.4472 0.7089 2.1562
HAT_B 225.7435 -0.9393 224.8042
001__G-SITE-013 HAT_OCC 0.9212 0.4453 1.3665
HAT_B 163.8727 -0.9562 162.9165
001__G-SITE-014 HAT_OCC 1.1805 0.4887 1.6692
HAT_B 264.7068 -0.5238 264.1831
001__G-SITE-015 HAT_OCC 1.3148 0.5880 1.9028
HAT_B 250.8974 -1.0426 249.8548
001__G-SITE-016 HAT_OCC 1.4841 0.6934 2.1775
HAT_B 300.0000 0.0000 300.0000 ->]
001__G-SITE-017 HAT_OCC 0.6966 0.3615 1.0581
HAT_B 300.0000 0.0000 300.0000 ->]
--------------------------------
The very next small cycle: B-factor of SITE 6 drops by about 75
001__G-SITE-001 HAT_OCC 1.7469 0.0017 1.7486
HAT_B 147.6785 -42.3724 105.3061
001__G-SITE-002 HAT_OCC 2.3100 -0.0154 2.2946
HAT_B 154.2601 -31.3099 122.9502
001__G-SITE-003 HAT_OCC 2.1847 -0.0207 2.1640
HAT_B 185.1180 8.1799 193.2979
001__G-SITE-004 HAT_OCC 2.0874 -0.0284 2.0590
HAT_B 197.8728 19.6576 217.5304
001__G-SITE-005 HAT_OCC 2.6413 0.0608 2.7021
HAT_B 213.4502 14.4088 227.8590
001__G-SITE-006 HAT_OCC 2.4041 0.0002 2.4044
HAT_B 153.3506 -75.3947 77.9559
001__G-SITE-007 HAT_OCC 1.7553 -0.0193 1.7360
HAT_B 173.7482 6.3321 180.0803
001__G-SITE-008 HAT_OCC 1.9932 0.0283 2.0215
HAT_B 184.9196 18.8103 203.7298
001__G-SITE-009 HAT_OCC 2.3595 0.0342 2.3937
HAT_B 192.9783 15.1212 208.0994
001__G-SITE-010 HAT_OCC 2.1437 -0.0026 2.1411
HAT_B 200.1083 11.6774 211.7856
001__G-SITE-011 HAT_OCC 2.1800 -0.0634 2.1166
HAT_B 166.3402 -56.0831 110.2571
001__G-SITE-012 HAT_OCC 2.1562 0.0179 2.1741
HAT_B 224.8042 38.3077 263.1119
001__G-SITE-013 HAT_OCC 1.3665 -0.0235 1.3430
HAT_B 162.9165 22.0442 184.9607
001__G-SITE-014 HAT_OCC 1.6692 0.0306 1.6998
HAT_B 264.1831 9.4390 273.6221
001__G-SITE-015 HAT_OCC 1.9028 0.0364 1.9392
HAT_B 249.8548 -4.5829 245.2718
001__G-SITE-016 HAT_OCC 2.1775 -0.0052 2.1722
HAT_B 300.0000 0.0000 300.0000 <-]
001__G-SITE-017 HAT_OCC 1.0581 0.0441 1.1022
HAT_B 300.0000 0.0000 300.0000 <-]
-------------------------------------
A few cycles later: B-factor of SITE 6 is now 1.0, and stays that way
001__G-SITE-001 HAT_OCC 0.9540 0.0608 1.0148
HAT_B 100.8967 2.4084 103.3051
001__G-SITE-002 HAT_OCC 1.3670 0.0974 1.4644
HAT_B 124.2807 -6.2762 118.0045
001__G-SITE-003 HAT_OCC 1.4122 0.0847 1.4969
HAT_B 165.5046 -13.7893 151.7153
001__G-SITE-004 HAT_OCC 1.3042 0.1374 1.4417
HAT_B 159.0778 14.0159 173.0936
001__G-SITE-005 HAT_OCC 1.8778 0.2253 2.1031
HAT_B 227.7046 -4.6517 223.0529
001__G-SITE-006 HAT_OCC 1.0219 -0.2701 0.7518
HAT_B 41.3661 -40.3661 1.0000 [<-
001__G-SITE-007 HAT_OCC 1.0922 0.0566 1.1488
HAT_B 150.3008 -15.5740 134.7268
001__G-SITE-008 HAT_OCC 1.4094 0.1122 1.5216
HAT_B 201.8194 -18.7466 183.0728
001__G-SITE-009 HAT_OCC 1.6166 0.2004 1.8171
HAT_B 201.2297 -4.5830 196.6467
001__G-SITE-010 HAT_OCC 1.4988 0.1621 1.6608
HAT_B 215.9288 -10.5880 205.3408
001__G-SITE-011 HAT_OCC 1.1856 0.0182 1.2038
HAT_B 103.9965 5.4042 109.4008
001__G-SITE-012 HAT_OCC 0.8806 0.0912 0.9717
HAT_B 55.0457 88.9120 143.9577
001__G-SITE-013 HAT_OCC 0.9247 0.1006 1.0253
HAT_B 155.5759 6.6344 162.2103
001__G-SITE-014 HAT_OCC 1.1636 0.2149 1.3785
HAT_B 287.3449 11.9467 299.2916
001__G-SITE-015 HAT_OCC 1.2764 0.0898 1.3662
HAT_B 238.9843 -36.9708 202.0135
001__G-SITE-016 HAT_OCC 1.3258 0.1084 1.4342
HAT_B 294.1810 -26.6462 267.5348
001__G-SITE-017 HAT_OCC 0.7161 0.1652 0.8813
HAT_B 300.0000 0.0000 300.0000 <-]
001_001_001_001 NANO_BGLO 0.0000 0.0000 0.0000 [<-
=================================
not refining occupancies(occup=1.0)
--------------------------------------------------------
first cycle of B-factor refinement: B-factor of SITE 6 drops by 152
001__G-SITE-001 HAT_B 149.2960 -79.1425 70.1535
001__G-SITE-002 HAT_B 155.8439 -46.2592 109.5847
001__G-SITE-003 HAT_B 186.3591 -12.7966 173.5625
001__G-SITE-004 HAT_B 199.2562 -34.9708 164.2854
001__G-SITE-005 HAT_B 213.9898 -22.3762 191.6136
001__G-SITE-006 HAT_B 155.2214 -152.6520 2.5694
001__G-SITE-007 HAT_B 174.7769 -11.0692 163.7076
001__G-SITE-008 HAT_B 185.8664 -52.2808 133.5855
001__G-SITE-009 HAT_B 193.9789 -32.2719 161.7070
001__G-SITE-010 HAT_B 200.6610 -16.0723 184.5886
001__G-SITE-011 HAT_B 168.2568 -60.1715 108.0853
001__G-SITE-012 HAT_B 225.7435 -138.1051 87.6384
001__G-SITE-013 HAT_B 163.8727 -15.9228 147.9499
001__G-SITE-014 HAT_B 264.7068 1.3815 266.0884
001__G-SITE-015 HAT_B 250.8974 -25.9098 224.9876
001__G-SITE-016 HAT_B 300.0000 -6.1918 293.8082
001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 <-]
------------
fourth cycle ("convergence")
001__G-SITE-001 HAT_B 92.8436 1.0171 93.8607 9.9228
001__G-SITE-002 HAT_B 119.0792 -0.3648 118.7144 8.7481
001__G-SITE-003 HAT_B 161.8942 5.2916 167.1858 11.5122
001__G-SITE-004 HAT_B 150.6342 3.9114 154.5456 11.5175
001__G-SITE-005 HAT_B 162.5293 4.9221 167.4514 10.9640
001__G-SITE-006 HAT_B 28.2706 12.8946 41.1652 2.8821
001__G-SITE-007 HAT_B 151.2232 4.0154 155.2387 13.1730
001__G-SITE-008 HAT_B 154.2849 3.8372 158.1221 11.7087
001__G-SITE-009 HAT_B 150.7050 2.1013 152.8063 11.0317
001__G-SITE-010 HAT_B 162.1460 6.4316 168.5776 12.3290
001__G-SITE-011 HAT_B 128.7785 3.6294 132.4079 8.5903
001__G-SITE-012 HAT_B 140.2975 21.5858 161.8834 10.1248
001__G-SITE-013 HAT_B 126.4959 -1.4780 125.0180 15.4597
001__G-SITE-014 HAT_B 223.7989 13.2720 237.0708 23.3402
001__G-SITE-015 HAT_B 154.6024 20.9541 175.5565 13.3123
001__G-SITE-016 HAT_B 236.7864 20.8837 257.6702 20.7670
001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 0.0000 ->]
-------------
last cycle (2 more small cycles)
001__G-SITE-001 HAT_B 87.9400 -5.2957 82.6443 12.1455
001__G-SITE-002 HAT_B 116.5185 -2.0488 114.4697 9.1728
001__G-SITE-003 HAT_B 167.9062 -0.4840 167.4222 11.8020
001__G-SITE-004 HAT_B 154.3282 -1.0146 153.3136 12.0092
001__G-SITE-005 HAT_B 168.5729 -0.4999 168.0730 11.3471
001__G-SITE-006 HAT_B 50.8219 5.8795 56.7014 5.8259
001__G-SITE-007 HAT_B 156.5339 -0.1544 156.3795 13.5625
001__G-SITE-008 HAT_B 158.7488 -0.4433 158.3056 12.1579
001__G-SITE-009 HAT_B 151.7882 -1.0714 150.7168 11.1549
001__G-SITE-010 HAT_B 169.1792 -0.2711 168.9081 12.8765
001__G-SITE-011 HAT_B 131.4322 -1.5125 129.9198 9.1421
001__G-SITE-012 HAT_B 167.3042 -0.7311 166.5730 13.2964
001__G-SITE-013 HAT_B 124.8798 -0.7616 124.1182 15.5111
001__G-SITE-014 HAT_B 238.3301 -0.2120 238.1182 25.2273
001__G-SITE-015 HAT_B 182.6898 1.4207 184.1104 16.7740
001__G-SITE-016 HAT_B 262.7511 -0.2747 262.4764 24.3344
001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 0.0000 ->]
============
From vonrhein@globalphasing.com Thu Jul 17 08:27:02 2003
From: vonrhein@globalphasing.com (Clemens Vonrhein)
Date: Thu, 17 Jul 2003 08:27:02 +0100
Subject: [sharp-discuss] very low B-factors
In-Reply-To: <3F3E4F1B@bearmail.berkeley.edu>
References: <3F3E4F1B@bearmail.berkeley.edu>
Message-ID: <20030717072702.GD2509@galois.globalphasing.com>
--8nsIa27JVQLqB7/C
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable
Dear Greg,
in my experience, B factors can go a bit funny at lowish resolution -
_if_ you also refine scaling B factors etc.=20
So could you please send us your whole SIN file? And have a look at
the values and the refinement behaviour of
SCAL_B
SCAL_B6_ADD
NISO_BGLO
NANO_BGLO
If SCAL_B parameters are going rather high (say > 5) I would probably
set them to zero and not refine/estimate them at all. Same for the
*_BGLO parameters.
And after your refinement (with or without fixed SCAL_B): what do the
residual maps look like? I know, it is nice if the values for
occupancy and B for sites come out at chemical meaningful
values. However, at this stage you are interested in getting a heavy
atom model that explains the differences (anomalous and dispersive)
well. So what I would do is
1. Have a look at the ANO residual maps for each wavelength will
tell you if the f'' values are correct. Since you use the same
HAT_OCC/HAT_B for both wavelengths (which makes sense) a wrong
f'' value at one wavelength can mess things up.
2. In the various residual maps, you would also see additional sites
(assuming that one of the 17 sites the one might be wrong).
3. Met sidechains quite often are disordered: any sign for that in
the residual maps? Also, N-terminal Met are often not visible.
4. Use autoSHARP (with the set of known sites) to run the whole
thing through to density modification. The difference in CC
between original and inverted hand will tell you if the HA model
is good. It will also give a whole lot of information (notes and
warnings - have a look at the warning messages!).
5. Why do you have a 2-wavelength MAD experiment? If this is because
your crystal slowly died (and you couldn't collect the third
wavelength) then I would tend to first do a SAD with the first
wavelength - and create a HA model that cleans up the residual
maps. Then add the second wavelength and see if it actually
helps.
6. Once you have done some density modification (and the CC between
the two hands is significantly different to be sure you have the
right hand) you can do 'ordinary' difference Fourier maps to get
a list of sites.
Hope that helps - let us know about any solution!
Cheers
Clemens
On Wed, Jul 16, 2003 at 05:42:35PM -0700, Gregory D. Bowman wrote:
> Hello -
>=20
> I am working with a 2-wavelength MAD dataset to about 3.2A resolution. Fr=
om a=20
> related crystal, I know the 17 Se sites pretty confidently, and these sit=
es=20
> seem to refine OK in SOLVE for the dataset I am having trouble with (so I=
am=20
> pretty sure the sites are all real). With SHARP, the B-factor of one site=
=20
> refines to 1.0. If I do not refine occupancies, the B-factor still dips p=
retty=20
> low in the first cycle (B=3D2.5) but manages to recover somewhat by the f=
inal=20
> cycle (B=3D56.7), though it is still relatively low for this resolution. =
Is it=20
> the case that I simply do not have enough information to refine these=20
> parameters at this resolution? Some of the logfile is below.
>=20
> Thanks for any advice.
>=20
> Greg
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D
> NOTE - site 6 is the offender. I apologise if the formatting does not car=
ry=20
> though in the email.
> -------------------------------------------------------
> refining both B and occupancies:
> --------------------------------
> First cycle of refining B/occupancies: Everything seems OK
>=20
>=20
> 001__G-SITE-001 HAT_OCC 1.1969 0.5500 1.7469
> HAT_B 149.2960 -1.6175 147.6785
> 001__G-SITE-002 HAT_OCC 1.5708 0.7393 2.3100
> HAT_B 155.8439 -1.5838 154.2601
> 001__G-SITE-003 HAT_OCC 1.5014 0.6834 2.1847
> HAT_B 186.3591 -1.2411 185.1180
> 001__G-SITE-004 HAT_OCC 1.4379 0.6495 2.0874
> HAT_B 199.2562 -1.3835 197.8728
> 001__G-SITE-005 HAT_OCC 1.8110 0.8303 2.6413
> HAT_B 213.9898 -0.5395 213.4502
>=20
> 001__G-SITE-006 HAT_OCC 1.6478 0.7564 2.4041
> HAT_B 155.2214 -1.8708 153.3506
>=20
> 001__G-SITE-007 HAT_OCC 1.1981 0.5572 1.7553
> HAT_B 174.7769 -1.0286 173.7482
> 001__G-SITE-008 HAT_OCC 1.3638 0.6294 1.9932
> HAT_B 185.8664 -0.9468 184.9196
> 001__G-SITE-009 HAT_OCC 1.6190 0.7405 2.3595
> HAT_B 193.9789 -1.0006 192.9783
> 001__G-SITE-010 HAT_OCC 1.4603 0.6834 2.1437
> HAT_B 200.6610 -0.5527 200.1083
> 001__G-SITE-011 HAT_OCC 1.4920 0.6880 2.1800
> HAT_B 168.2568 -1.9167 166.3402
> 001__G-SITE-012 HAT_OCC 1.4472 0.7089 2.1562
> HAT_B 225.7435 -0.9393 224.8042
> 001__G-SITE-013 HAT_OCC 0.9212 0.4453 1.3665
> HAT_B 163.8727 -0.9562 162.9165
> 001__G-SITE-014 HAT_OCC 1.1805 0.4887 1.6692
> HAT_B 264.7068 -0.5238 264.1831
> 001__G-SITE-015 HAT_OCC 1.3148 0.5880 1.9028
> HAT_B 250.8974 -1.0426 249.8548
> 001__G-SITE-016 HAT_OCC 1.4841 0.6934 2.1775
> HAT_B 300.0000 0.0000 300.0000 ->]
> 001__G-SITE-017 HAT_OCC 0.6966 0.3615 1.0581
> HAT_B 300.0000 0.0000 300.0000 ->]
> --------------------------------
> The very next small cycle: B-factor of SITE 6 drops by about 75
>=20
> 001__G-SITE-001 HAT_OCC 1.7469 0.0017 1.7486
> HAT_B 147.6785 -42.3724 105.3061
> 001__G-SITE-002 HAT_OCC 2.3100 -0.0154 2.2946
> HAT_B 154.2601 -31.3099 122.9502
> 001__G-SITE-003 HAT_OCC 2.1847 -0.0207 2.1640
> HAT_B 185.1180 8.1799 193.2979
> 001__G-SITE-004 HAT_OCC 2.0874 -0.0284 2.0590
> HAT_B 197.8728 19.6576 217.5304
> 001__G-SITE-005 HAT_OCC 2.6413 0.0608 2.7021
> HAT_B 213.4502 14.4088 227.8590
>=20
> 001__G-SITE-006 HAT_OCC 2.4041 0.0002 2.4044
> HAT_B 153.3506 -75.3947 77.9559
>=20
> 001__G-SITE-007 HAT_OCC 1.7553 -0.0193 1.7360
> HAT_B 173.7482 6.3321 180.0803
> 001__G-SITE-008 HAT_OCC 1.9932 0.0283 2.0215
> HAT_B 184.9196 18.8103 203.7298
> 001__G-SITE-009 HAT_OCC 2.3595 0.0342 2.3937
> HAT_B 192.9783 15.1212 208.0994
> 001__G-SITE-010 HAT_OCC 2.1437 -0.0026 2.1411
> HAT_B 200.1083 11.6774 211.7856
> 001__G-SITE-011 HAT_OCC 2.1800 -0.0634 2.1166
> HAT_B 166.3402 -56.0831 110.2571
> 001__G-SITE-012 HAT_OCC 2.1562 0.0179 2.1741
> HAT_B 224.8042 38.3077 263.1119
> 001__G-SITE-013 HAT_OCC 1.3665 -0.0235 1.3430
> HAT_B 162.9165 22.0442 184.9607
> 001__G-SITE-014 HAT_OCC 1.6692 0.0306 1.6998
> HAT_B 264.1831 9.4390 273.6221
> 001__G-SITE-015 HAT_OCC 1.9028 0.0364 1.9392
> HAT_B 249.8548 -4.5829 245.2718
> 001__G-SITE-016 HAT_OCC 2.1775 -0.0052 2.1722
> HAT_B 300.0000 0.0000 300.0000 <-]
> 001__G-SITE-017 HAT_OCC 1.0581 0.0441 1.1022
> HAT_B 300.0000 0.0000 300.0000 <-]
> -------------------------------------
> A few cycles later: B-factor of SITE 6 is now 1.0, and stays that way
>=20
> 001__G-SITE-001 HAT_OCC 0.9540 0.0608 1.0148
> HAT_B 100.8967 2.4084 103.3051
> 001__G-SITE-002 HAT_OCC 1.3670 0.0974 1.4644
> HAT_B 124.2807 -6.2762 118.0045
> 001__G-SITE-003 HAT_OCC 1.4122 0.0847 1.4969
> HAT_B 165.5046 -13.7893 151.7153
> 001__G-SITE-004 HAT_OCC 1.3042 0.1374 1.4417
> HAT_B 159.0778 14.0159 173.0936
> 001__G-SITE-005 HAT_OCC 1.8778 0.2253 2.1031
> HAT_B 227.7046 -4.6517 223.0529
>=20
> 001__G-SITE-006 HAT_OCC 1.0219 -0.2701 0.7518
> HAT_B 41.3661 -40.3661 1.0000 [<-
>=20
> 001__G-SITE-007 HAT_OCC 1.0922 0.0566 1.1488
> HAT_B 150.3008 -15.5740 134.7268
> 001__G-SITE-008 HAT_OCC 1.4094 0.1122 1.5216
> HAT_B 201.8194 -18.7466 183.0728
> 001__G-SITE-009 HAT_OCC 1.6166 0.2004 1.8171
> HAT_B 201.2297 -4.5830 196.6467
> 001__G-SITE-010 HAT_OCC 1.4988 0.1621 1.6608
> HAT_B 215.9288 -10.5880 205.3408
> 001__G-SITE-011 HAT_OCC 1.1856 0.0182 1.2038
> HAT_B 103.9965 5.4042 109.4008
> 001__G-SITE-012 HAT_OCC 0.8806 0.0912 0.9717
> HAT_B 55.0457 88.9120 143.9577
> 001__G-SITE-013 HAT_OCC 0.9247 0.1006 1.0253
> HAT_B 155.5759 6.6344 162.2103
> 001__G-SITE-014 HAT_OCC 1.1636 0.2149 1.3785
> HAT_B 287.3449 11.9467 299.2916
> 001__G-SITE-015 HAT_OCC 1.2764 0.0898 1.3662
> HAT_B 238.9843 -36.9708 202.0135
> 001__G-SITE-016 HAT_OCC 1.3258 0.1084 1.4342
> HAT_B 294.1810 -26.6462 267.5348
> 001__G-SITE-017 HAT_OCC 0.7161 0.1652 0.8813
> HAT_B 300.0000 0.0000 300.0000 <-]
> 001_001_001_001 NANO_BGLO 0.0000 0.0000 0.0000 [<-
>=20
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D
> not refining occupancies(occup=3D1.0)
> --------------------------------------------------------
> first cycle of B-factor refinement: B-factor of SITE 6 drops by 152
>=20
> 001__G-SITE-001 HAT_B 149.2960 -79.1425 70.1535
> 001__G-SITE-002 HAT_B 155.8439 -46.2592 109.5847
> 001__G-SITE-003 HAT_B 186.3591 -12.7966 173.5625
> 001__G-SITE-004 HAT_B 199.2562 -34.9708 164.2854
> 001__G-SITE-005 HAT_B 213.9898 -22.3762 191.6136
>=20
> 001__G-SITE-006 HAT_B 155.2214 -152.6520 2.5694
>=20
> 001__G-SITE-007 HAT_B 174.7769 -11.0692 163.7076
> 001__G-SITE-008 HAT_B 185.8664 -52.2808 133.5855
> 001__G-SITE-009 HAT_B 193.9789 -32.2719 161.7070
> 001__G-SITE-010 HAT_B 200.6610 -16.0723 184.5886
> 001__G-SITE-011 HAT_B 168.2568 -60.1715 108.0853
> 001__G-SITE-012 HAT_B 225.7435 -138.1051 87.6384
> 001__G-SITE-013 HAT_B 163.8727 -15.9228 147.9499
> 001__G-SITE-014 HAT_B 264.7068 1.3815 266.0884
> 001__G-SITE-015 HAT_B 250.8974 -25.9098 224.9876
> 001__G-SITE-016 HAT_B 300.0000 -6.1918 293.8082
> 001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 <-]
>=20
> ------------
>=20
> fourth cycle ("convergence")
> 001__G-SITE-001 HAT_B 92.8436 1.0171 93.8607 9.9228
>=20
> 001__G-SITE-002 HAT_B 119.0792 -0.3648 118.7144 8.7481
>=20
> 001__G-SITE-003 HAT_B 161.8942 5.2916 167.1858 11.5122
>=20
> 001__G-SITE-004 HAT_B 150.6342 3.9114 154.5456 11.5175
>=20
> 001__G-SITE-005 HAT_B 162.5293 4.9221 167.4514 10.9640
>=20
>=20
> 001__G-SITE-006 HAT_B 28.2706 12.8946 41.1652 2.8821
>=20
>=20
> 001__G-SITE-007 HAT_B 151.2232 4.0154 155.2387 13.1730
>=20
> 001__G-SITE-008 HAT_B 154.2849 3.8372 158.1221 11.7087
>=20
> 001__G-SITE-009 HAT_B 150.7050 2.1013 152.8063 11.0317
>=20
> 001__G-SITE-010 HAT_B 162.1460 6.4316 168.5776 12.3290
>=20
> 001__G-SITE-011 HAT_B 128.7785 3.6294 132.4079 8.5903
>=20
> 001__G-SITE-012 HAT_B 140.2975 21.5858 161.8834 10.1248
>=20
> 001__G-SITE-013 HAT_B 126.4959 -1.4780 125.0180 15.4597
>=20
> 001__G-SITE-014 HAT_B 223.7989 13.2720 237.0708 23.3402
>=20
> 001__G-SITE-015 HAT_B 154.6024 20.9541 175.5565 13.3123
>=20
> 001__G-SITE-016 HAT_B 236.7864 20.8837 257.6702 20.7670
>=20
> 001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 0.0000=
->]
>=20
> -------------
> last cycle (2 more small cycles)
>=20
> 001__G-SITE-001 HAT_B 87.9400 -5.2957 82.6443 12.1455
>=20
> 001__G-SITE-002 HAT_B 116.5185 -2.0488 114.4697 9.1728
>=20
> 001__G-SITE-003 HAT_B 167.9062 -0.4840 167.4222 11.8020
>=20
> 001__G-SITE-004 HAT_B 154.3282 -1.0146 153.3136 12.0092
>=20
> 001__G-SITE-005 HAT_B 168.5729 -0.4999 168.0730 11.3471
>=20
>=20
> 001__G-SITE-006 HAT_B 50.8219 5.8795 56.7014 5.8259
>=20
>=20
> 001__G-SITE-007 HAT_B 156.5339 -0.1544 156.3795 13.5625
>=20
> 001__G-SITE-008 HAT_B 158.7488 -0.4433 158.3056 12.1579
>=20
> 001__G-SITE-009 HAT_B 151.7882 -1.0714 150.7168 11.1549
>=20
> 001__G-SITE-010 HAT_B 169.1792 -0.2711 168.9081 12.8765
>=20
> 001__G-SITE-011 HAT_B 131.4322 -1.5125 129.9198 9.1421
>=20
> 001__G-SITE-012 HAT_B 167.3042 -0.7311 166.5730 13.2964
>=20
> 001__G-SITE-013 HAT_B 124.8798 -0.7616 124.1182 15.5111
>=20
> 001__G-SITE-014 HAT_B 238.3301 -0.2120 238.1182 25.2273
>=20
> 001__G-SITE-015 HAT_B 182.6898 1.4207 184.1104 16.7740
>=20
> 001__G-SITE-016 HAT_B 262.7511 -0.2747 262.4764 24.3344
>=20
> 001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 0.0000=
->]
>=20
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>=20
>=20
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
--=20
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT 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)
***************************************************************
--8nsIa27JVQLqB7/C
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From zzjqd@mail.ustc.edu.cn Tue Jul 29 07:34:27 2003
From: zzjqd@mail.ustc.edu.cn (zijie zhou)
Date: Tue, 29 Jul 2003 14:34:27 +0800 (CST)
Subject: [sharp-discuss] why not found licence
Message-ID: <1888.202.38.91.97.1059460467.squirrel@webmail.ustc.edu.cn>
Dear sharp users:
I installed the sharp and try to run the accompanied example
(kr-know-site). I get the following message:
This program will not run on this system.
Please contact the SHARP Developers
for assistance. Include this error message and your $BDG_home/.licence file.
--------------------------------------------------------------------------------
***SHARP=ERR=+0003: Licence not found! ***
Why it complained that the licence is not found. My .licence file is
indeed in $BDG_home.
Your help is highly appreciated!
--
*************************************************************
Zhaocai Zhou
School of Life Sciences,
University of Science & Technology of China;
Key Laboratory of Structural Biology,
Chinese Academy of Sciences, Hefei, Anhui, 230026, P.R.China
Tel:86-551-3607334
Fax:86-551-3607154
*************************************************************
From vonrhein@globalphasing.com Tue Jul 29 10:13:49 2003
From: vonrhein@globalphasing.com (Clemens Vonrhein)
Date: Tue, 29 Jul 2003 10:13:49 +0100
Subject: [sharp-discuss] why not found licence
In-Reply-To: <1888.202.38.91.97.1059460467.squirrel@webmail.ustc.edu.cn>
References: <1888.202.38.91.97.1059460467.squirrel@webmail.ustc.edu.cn>
Message-ID: <20030729091349.GB17860@galois.globalphasing.com>
--lEGEL1/lMxI0MVQ2
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable
Dear Zhaocai,
remember that you need a licence key for each machine you want to run
the software on. The initial licence request will cover your
departement/lab (and include usually a licence key for one
machine). More licence keys (for this initial licence request) can be
requested at
http://www.globalphasing.com/sharp/
Hope that helps.
Cheers
Clemens
On Tue, Jul 29, 2003 at 02:34:27PM +0800, zijie zhou wrote:
> Dear sharp users:
>=20
> I installed the sharp and try to run the accompanied example
> (kr-know-site). I get the following message:
>=20
>=20
> This program will not run on this system.
> Please contact the SHARP Developers
> for assistance. Include this error message and your $BDG_home/.licence fi=
le.
>=20
>=20
>=20
> -------------------------------------------------------------------------=
-------
>=20
>=20
> ***SHARP=3DERR=3D+0003: Licence not found! ***
>=20
>=20
> Why it complained that the licence is not found. My .licence file is
> indeed in $BDG_home.
>=20
> Your help is highly appreciated!
>=20
>=20
>=20
>=20
>=20
> --=20
> *************************************************************
> Zhaocai Zhou
> School of Life Sciences,
> University of Science & Technology of China;
> Key Laboratory of Structural Biology,
> Chinese Academy of Sciences, Hefei, Anhui, 230026, P.R.China
> Tel:86-551-3607334
> Fax:86-551-3607154
> *************************************************************
>=20
>=20
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
--=20
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT 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)
***************************************************************
--lEGEL1/lMxI0MVQ2
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From zzjqd@mail.ustc.edu.cn Wed Jul 30 14:09:31 2003
From: zzjqd@mail.ustc.edu.cn (zijie zhou)
Date: Wed, 30 Jul 2003 21:09:31 +0800 (CST)
Subject: [sharp-discuss] why not found licence
In-Reply-To: <20030729091349.GB17860@galois.globalphasing.com>
References: <1888.202.38.91.97.1059460467.squirrel@webmail.ustc.edu.cn>
<20030729091349.GB17860@galois.globalphasing.com>
Message-ID: <2703.202.38.91.97.1059570571.squirrel@webmail.ustc.edu.cn>
hi,
I applied a new licence and put it in the $BDG home. But I get another
error this time. The error message is like this:
"Error: in running sharp"
No other information was observed. Through "top" command, I see the sharp
is in ready state. But the program can not go forward.(I am sure it was
locked or died)
The program can go smoothly at the first stage including preparinng and
analysis of the raw data. It give error message when it begin to find
heavy atom sites.
thanks a lot.
zhaocai
Clemens Vonrhein дµÀ:
> Dear Zhaocai,
>
> remember that you need a licence key for each machine you want to run
> the software on. The initial licence request will cover your
> departement/lab (and include usually a licence key for one
> machine). More licence keys (for this initial licence request) can be
> requested at
>
> http://www.globalphasing.com/sharp/
>
> Hope that helps.
>
> Cheers
>
> Clemens
>
> On Tue, Jul 29, 2003 at 02:34:27PM +0800, zijie zhou wrote:
>> Dear sharp users:
>>
>> I installed the sharp and try to run the accompanied example
>> (kr-know-site). I get the following message:
>>
>>
>> This program will not run on this system.
>> Please contact the SHARP Developers
>> for assistance. Include this error message and your $BDG_home/.licence
>> file.
>>
>>
>>
>> --------------------------------------------------------------------------------
>>
>>
>> ***SHARP=ERR=+0003: Licence not found! ***
>>
>>
>> Why it complained that the licence is not found. My .licence file is
>> indeed in $BDG_home.
>>
>> Your help is highly appreciated!
>>
>>
>>
>>
>>
>> --
>> *************************************************************
>> Zhaocai Zhou
>> School of Life Sciences,
>> University of Science & Technology of China;
>> Key Laboratory of Structural Biology,
>> Chinese Academy of Sciences, Hefei, Anhui, 230026, P.R.China
>> Tel:86-551-3607334
>> Fax:86-551-3607154
>> *************************************************************
>>
>>
>> _______________________________________________
>> sharp-discuss mailing list
>> sharp-discuss@globalphasing.com
>> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
>
> --
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT 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)
> ***************************************************************
>
--
*************************************************************
Zhaocai Zhou
School of Life Sciences,
University of Science & Technology of China;
Key Laboratory of Structural Biology,
Chinese Academy of Sciences, Hefei, Anhui, 230026, P.R.China
Tel:86-551-3607334
Fax:86-551-3607154
*************************************************************
From vonrhein@globalphasing.com Wed Jul 30 15:04:48 2003
From: vonrhein@globalphasing.com (Clemens Vonrhein)
Date: Wed, 30 Jul 2003 15:04:48 +0100
Subject: [sharp-discuss] why not found licence
In-Reply-To: <2703.202.38.91.97.1059570571.squirrel@webmail.ustc.edu.cn>
References: <1888.202.38.91.97.1059460467.squirrel@webmail.ustc.edu.cn> <20030729091349.GB17860@galois.globalphasing.com> <2703.202.38.91.97.1059570571.squirrel@webmail.ustc.edu.cn>
Message-ID: <20030730140447.GG30977@galois.globalphasing.com>
--nhYGnrYv1PEJ5gA2
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable
Dear zhaocai,
the fact that autoSHARP is dying during heavy atom detection is due to
an error in your .licence file (still). You can test your .licence
file like this:
% cd /where/ever
% ls -l .licence
% setenv BDG_home `pwd` # for csh/tcsh
- or -
% BDG_home=3D`pwd` && export BDG_home # for sh/bash/ksh
% bin/linux_exe/sharp # for Intel/Linux
- or -
% bin/alpha_exe/sharp # for Alpha/Tru64 (OSF1)
- or -
% bin/irixn2_exe/sharp # for SGI/Irix
The last step will give an error (something along the line of
parameter file not found). But it should NOT give a licencing
error. If it does:
1. are you sure you saved the .licence file attachement as-is in
$BDG_home? No editing is allowed (whis will invalidate the
licence key).
2. check the .licence file for 'funny' characters (load it into
more, less, vi and emacs)
3. make sure you use the '.licence' spelling
Hope that helps
Cheers
Clemens
On Wed, Jul 30, 2003 at 09:09:31PM +0800, zijie zhou wrote:
> hi,
> I applied a new licence and put it in the $BDG home. But I get another
> error this time. The error message is like this:
> "Error: in running sharp"
> No other information was observed. Through "top" command, I see the sharp
> is in ready state. But the program can not go forward.(I am sure it was
> locked or died)
> The program can go smoothly at the first stage including preparinng and
> analysis of the raw data. It give error message when it begin to find
> heavy atom sites.
> thanks a lot.
> zhaocai
>=20
> Clemens Vonrhein ????:
>=20
> > Dear Zhaocai,
> >
> > remember that you need a licence key for each machine you want to run
> > the software on. The initial licence request will cover your
> > departement/lab (and include usually a licence key for one
> > machine). More licence keys (for this initial licence request) can be
> > requested at
> >
> > http://www.globalphasing.com/sharp/
> >
> > Hope that helps.
> >
> > Cheers
> >
> > Clemens
> >
> > On Tue, Jul 29, 2003 at 02:34:27PM +0800, zijie zhou wrote:
> >> Dear sharp users:
> >>
> >> I installed the sharp and try to run the accompanied example
> >> (kr-know-site). I get the following message:
> >>
> >>
> >> This program will not run on this system.
> >> Please contact the SHARP Developers
> >> for assistance. Include this error message and your $BDG_home/.licence
> >> file.
> >>
> >>
> >>
> >> ----------------------------------------------------------------------=
----------
> >>
> >>
> >> ***SHARP=3DERR=3D+0003: Licence not found! ***
> >>
> >>
> >> Why it complained that the licence is not found. My .licence file is
> >> indeed in $BDG_home.
> >>
> >> Your help is highly appreciated!
> >>
> >>
> >>
> >>
> >>
> >> --
> >> *************************************************************
> >> Zhaocai Zhou
> >> School of Life Sciences,
> >> University of Science & Technology of China;
> >> Key Laboratory of Structural Biology,
> >> Chinese Academy of Sciences, Hefei, Anhui, 230026, P.R.China
> >> Tel:86-551-3607334
> >> Fax:86-551-3607154
> >> *************************************************************
> >>
> >>
> >> _______________________________________________
> >> sharp-discuss mailing list
> >> sharp-discuss@globalphasing.com
> >> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
> >
> > --
> >
> > ***************************************************************
> > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT 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)
> > ***************************************************************
> >
>=20
>=20
> --=20
> *************************************************************
> Zhaocai Zhou
> School of Life Sciences,
> University of Science & Technology of China;
> Key Laboratory of Structural Biology,
> Chinese Academy of Sciences, Hefei, Anhui, 230026, P.R.China
> Tel:86-551-3607334
> Fax:86-551-3607154
> *************************************************************
--=20
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT 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)
***************************************************************
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