[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###############################################################
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### CCP PROGRAM SUITE: PEAKMAX VERSION 4L1: 08/08/00##
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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
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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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