Hi Li Chen, try
#!/bin/sh -f
sc xyzin 1XOU.pdb << eof-sc
Molecule 1
CHAIN A
MOLECULE 2
CHAIN B
end
eof-sc
in a small script lets say "sc.com"
then run %sc.com |tee sc.log
and you'll get something like this :
Summary of results:
________________________________________________________
D(A->B) D(B->A) D(A->B)+D(B->A)/2
Mean 0.679 0.686 0.682
Median 0.581 0.580 0.581
S(A->B) S(B->A) S(A->B)+S(B->A)/2
Mean 0.634 0.629 0.631
Median 0.684 0.682 0.683
Shape complementarity statistic Sc = 0.683
________________________________________________________
Logfile attached !!
:)
cheers
Stefan
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Li
Chen
Gesendet: Mittwoch, 1. Juni 2011 15:18
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Calculating shape complementarity (sc) parameter using
CCP4
Dear all,
I am trying to use the sc program in CCP4 suite the calculate the shape
complementarity parameter, but there is problem with reading the PDB file.
Unfortunately the "examples" webpage is not active anymore so I have no idea
how to fix it.
I attached the output log as follows:
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.1: SC version 6.1 : 17/09/07##
###############################################################
User: li Run date: 30/ 5/2011 Run time: 20:18:39
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>
Sc (Version 2.0): A program for determining Shape Complementarity
Copyright Michael Lawrence, Biomolecular Research Institute
343 Royal Parade Parkville Victoria Australia
This program is designed to compute Sc between two molecules.
It also allows the normal products to be "merged" into grasp surface files
for display in grasp.
___________________________________________________________________
FORMATTED OLD file opened on unit 7
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SCRADII, Filename:
/home/li/NMRsoftwareInstruction/CCP4/ccp4-6.1.13/lib/data/sc_radii.lib
<!--SUMMARY_END--></FONT></B>
Number of radii read from sc_radii file: 78
Opening PDB input file with logical name XYZIN
Logical name: XYZIN File name: 1XOU.pdb
PDB file is being opened on unit 1 for INPUT.
MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
RF RO
0.028 -0.000 -0.000 -0.000 35.422 0.000 0.000 -0.000
-0.000 0.014 -0.000 0.000 0.000 72.383 0.000 0.000
0.000 -0.000 0.010 -0.000 0.000 0.000 95.679 -0.000
-0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
UNFORMATTED SCRATCH file opened on unit 7
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SCTEMP, Filename: /tmp/li/sc_dots.09428
<!--SUMMARY_END--></FONT></B>
Number of atoms read from PDB file: 1238
GRASP mode disabled - no Grasp output will be produced
Selection commands:
-------------------
molecule 1
Molecule 1
molecule 2
Molecule 2
chain A
Number of atoms selected in chain A = 565
chain B
Number of atoms selected in chain B = 673
zone A 170 B 24
Number of atoms selected in zone = 345
at_excl A 170 N
Atom A 170 N excluded
end
Parameter values
----------------
Dot density : 15.00 per square Angstrom
Interface separation : 8.00 Angstroms
Trim width : 1.50 Angstroms
Probe radius : 1.70 Angstroms
Weight factor : 0.50 per square Angstrom
Selected atoms:
---------------
Number of atoms for first molecule 0
Number of atoms for second molecule 1237
Total number of atoms 1237
Setting up atoms for surfacing:
Potential interface atoms 0
Blocked atoms 1237
Atoms in Molecule 1 0
Atoms in Molecule 2 1237
Output diagnostics from Connolly subroutine MDS:
UNFORMATTED SCRATCH file opened on unit 7
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SCDOTS, Filename: /tmp/li/sc_dots.09428
<!--SUMMARY_END--></FONT></B>
Number of surface points:
Convex 0
Toroidal 0
Concave 0
Total 0
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
SC: No atoms found in interface.
SC: No atoms found in interface.
Times: User: 0.1s System: 0.0s Elapsed: 0:55
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
I also attach the PDB file I used for the calculate. Could you please have a
look at the output log and the PDB file and let me know what the problem is?
Thank you very much in advance.
Best regards
Sincerely,
Li Chen
sc.log
Description: Binary data
