[sharp-discuss] - peak list from residual map
Clemens Vonrhein
vonrhein@globalphasing.com
Wed, 13 Mar 2002 17:22:15 +0000
Hi,
now I see: your CCP4 programs report a version string
### 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
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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