[sharp-discuss] - peak list from residual map

Venkataraman Kabaleeswaran vkabale@uoft02.utoledo.edu
Wed, 13 Mar 2002 12:05:49 -0500


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 
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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.


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  (Q)QOPEN: file opened on unit  1      Status: READONLY
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 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
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 Logical name: XYZOUT, Filename: /tmp/26662.dir/peaks.pdb
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 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



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 PEAKMAX:   Normal Termination of PEAKMAX
 Times: User:       0.0s System:    0.0s Elapsed:    0:00
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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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