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
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