[sharp-discuss] - peak list from residual map
Clemens Vonrhein
vonrhein@globalphasing.com
Wed, 13 Mar 2002 18:26:45 +0000
Hi,
I suspected that ... maybe I have to discuss this with Kevin. I see if
I can think of a working fix for the current Sushi version - and let
you knoq about it. Probably not before tomorrow.
Cheers
Clemens
On Wed, Mar 13, 2002 at 01:09:53PM -0500, Venkataraman Kabaleeswaran wrote:
>
> Dear Clemens
>
> On Wednesday 13 March 2002 12:22 pm, you wrote:
> > Hi,
> >
> > now I see: your CCP4 programs report a version string
> >
>
> we use ccp4 for linux from Kevin Cowtan, information about this version can
> be found at http://www.ysbl.york.ac.uk/~cowtan/ccp4/ccp4.html
>
> We use this version because the official version (4.1.x) does not work
> correctly with redhat 7.2 and this one does. We verfied these results
> against those obtained on our SGI to determine that Cowtan's version worked
> vs the official release.
>
> I did not experience this problem with sharp 2.0
>
> > ### CCP PROGRAM SUITE: PEAKMAX VERSION 4L1: 08/08/00##
> > ^^^
> >
> > when it should be
> >
> > ### CCP PROGRAM SUITE: PEAKMAX VERSION 4.1: 08/08/00##
> >
> >
> > I'm puzzled how this could happen: your local version of CCP4 must
> > have had changes done to $CCP4/lib/src/ccplib.f (s/r CCP4_VERSION)!?
> > But why ... I'm puzzled. The 'normal' CCP4 distribution will always
> > report '4.1' for a CCP4 4.1x version.
> >
> > Cheers
> >
> > Clemens
>
> thanks
>
> venkataraman
>
> > On Wed, Mar 13, 2002 at 12:05:49PM -0500, Venkataraman Kabaleeswaran wrote:
> > > Dear clemens
> > >
> > > Thanks , Now I can view the residual map through SHARP after fixing
> > > the $BDG_home/bin/helpers.local file, it works fine now.
> > >
> > > here is the Peaks.log file
> > > -------------------------------------------------------------------------
> > >--------------------------------------------------------------------------
> > >---------
> > >
> > >
> > >
> > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> > > <pre>
> > >
> > >
> > >
> > >
> > > 1###############################################################
> > > ###############################################################
> > > ###############################################################
> > > ### CCP PROGRAM SUITE: PEAKMAX VERSION 4L1: 08/08/00##
> > > ###############################################################
> > > User: Run date: 8/ 3/02 Run time: 9:29:49
> > >
> > >
> > > Please reference: Collaborative Computational Project, Number 4. 1994.
> > > "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
> > > 760-763.
> > >
> > > as well as any specific reference in the program write-up.
> > >
> > >
> > > <!--SUMMARY_END--></FONT></B>
> > >
> > > (Q)QOPEN: file opened on unit 1 Status: READONLY
> > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> > > Logical Name: MAPIN Filename: /tmp/26662.dir/RESID.1.map
> > > <!--SUMMARY_END--></FONT></B>
> > >
> > >
> > > File name for input map file on unit 3 : /tmp/26662.dir/RESID.1.map
> > > file size = 365344 ; logical name MAPIN
> > >
> > >
> > > Number of columns, rows, sections ............... 65 56
> > > 25 Map mode ........................................ 2 Start and stop
> > > points on columns, rows, sections 0 64 0 55 0 24
> > > Grid sampling on x, y, z ........................ 110 48
> > > 64 Cell dimensions ................................. 72.41801 30.19900
> > > 43.32600 90.00000 100.11200 90.00000
> > > Fast, medium, slow axes ......................... Z X
> > > Y Minimum density ................................. -3.20004 Maximum
> > > density ................................. 2.69173 Mean density
> > > .................................... -0.00011 Rms deviation from mean
> > > density ................. 0.59274 Space-group
> > > ..................................... 5 Number of titles
> > > ................................ 1
> > >
> > > Titles :
> > > Map from fft
> > >
> > >
> > > Symmetry operations: X, Y, Z
> > > Symmetry operations: -X, Y, -Z
> > > Symmetry operations: X+1/2, Y+1/2, Z
> > > Symmetry operations: -X+1/2, Y+1/2, -Z
> > > Data line--- THRESHOLD RMS 3 NEGATIVES
> > > Data line--- NUMPEAKS 50
> > > Data line--- END
> > >
> > > Find 50 highest peaks above 1.778
> > >
> > >
> > > Orthogonalisation code 1: A // XO, C* // ZO (Standard Brookhaven)
> > >
> > >
> > > STANDARD PDB COORDINATE SETTING WILL BE ASSUMED
> > > IF NO SCALE CARDS PRESENT IN INPUT COORDINATE FILE
> > >
> > > Transformation matrix Fractional to orthogonal
> > >
> > > 72.4180 0.0000 -7.6068
> > > 0.0000 30.1990 0.0001
> > > 0.0000 0.0000 42.6530
> > >
> > > Entire map is to be searched
> > >
> > >
> > > FORMATTED UNKNOWN file opened on unit 7
> > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> > > Logical name: XYZOUT, Filename: /tmp/26662.dir/peaks.pdb
> > > <!--SUMMARY_END--></FONT></B>
> > >
> > >
> > > List of peaks in order of location
> > > ==================================
> > >
> > > Peaks related by symmetry are assigned the same site number
> > >
> > > Count Site Height Grid Fractional coordinates Orthogonal
> > > coordinates
> > >
> > > 1 1 1.92 10 0 11 0.0886 0.0000 0.1732 5.10 0.00
> > > 7.39 2 2 -1.91 48 0 18 0.4392 0.0000 0.2853 29.64 0.00
> > > 12.17 ......
> > > ......
> > > 107 1 1.92 45 24 53 0.4114 0.5000 0.8268 23.51 15.10
> > > 35.27
> > >
> > >
> > >
> > > There are 107 peaks higher than the threshold 1.77821 ( 3.00000
> > > *sigma)
> > >
> > > These peaks are sorted into descending order of height, the top 50 are
> > > selected for output
> > > The number of symmertry related peaks rejected for being too close to
> > > the map edge is 9
> > > Peaks related by symmetry are assigned the same site number
> > >
> > > Order No. Site Height/Rms Grid Fractional coordinates
> > > Orthogonal coordinates
> > >
> > > 1 70 68 -5.40 50 20 18 0.4585 0.4111 0.2793 31.08
> > > 12.42 11.91
> > > 2 69 67 -5.34 49 20 15 0.4437 0.4250 0.2325 30.36
> > > 12.84 9.92
> > > ....
> > > ...
> > > 50 1 1 3.24 10 0 11 0.0886 0.0000 0.1732 5.10
> > > 0.00 7.39
> > >
> > >
> > >
> > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> > > PEAKMAX: Normal Termination of PEAKMAX
> > > Times: User: 0.0s System: 0.0s Elapsed: 0:00
> > > </pre>
> > > <!--SUMMARY_END--></FONT></B>
> > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> > > </html>
> > > <!--SUMMARY_END--></FONT></B>
> > > -------------------------------------------------------------------------
> > >--------------------------------------------------------------------------
> > >----------------------
> > >
> > > On Wednesday 13 March 2002 03:00 am, you wrote:
> > > > Dear Venkataraman,
> > > >
> > > > > Yes, I viewed the residual map using O without any problem.
> > > > > But I could not view it through SHARP because it was searching for
> > > > > the menu, startup files for O in the wrong dir.
> > > > > "/usr/local/O/data/menu.odb" instead of right dir
> > > > > "/usr/pgm/08.0/menu.odb."
> > > >
> > > > Have you configured your helpers correctly? See the documentation -
> > > > either from your SHARP Control Panel or online at
> > > > http://www.globalphasing.com/sharp/installation/bdg/chapter0.html). In
> > > > short, you need to create and edit the $BDG_home/bin/helpers.local
> > > > file based on the $BDG_home/bin/helpers.local_template. Also, make
> > > > sure that your personal ~/.mailcap file is properly used.
> > > >
> > > > > I am using the perl5 (revision 5.0 version 6 subversion 0) version.
> > > >
> > > > That's fine then.
> > > >
> > > > > Yes I changed the rms limits for peak picking.
> > > >
> > > > I found that using a value of -3.0 works fine (picking all peaks above
> > > > +3.0 RMS and below -3.0 RMS).
> > > >
> > > > > Peaks.log file has full list of peaks end up with normal termination.
> > > >
> > > > Could you send me (not the list) this file?
> > > >
> > > > Cheers
> > > >
> > > > Clemens
> > >
> > > ---------
> > >
> > > _______________________________________________
> > > sharp-discuss mailing list
> > > sharp-discuss@globalphasing.com
> > > http://www.globalphasing.com/mailman/listinfo/sharp-discuss
--
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