[sharp-discuss] - peak list from residual map
Venkataraman Kabaleeswaran
vkabale@uoft02.utoledo.edu
Wed, 13 Mar 2002 13:09:53 -0500
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
> >
> > ---------
> >
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