hi all, I used the SC binary program to calculate shape complementary between two protein domains. It seems that SC runs properly. But, I can not find out output values of SC in the log file.
I attached the output log as follows. I also check two files in the /tmp/jzheng/sc_dots.14274, they are binary files, which are not readable for me. <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> <html> <!-- CCP4 HTML LOGFILE --> <hr> <!--SUMMARY_END--></FONT></B> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> <pre> ############################################################### ############################################################### ############################################################### ### CCP4 6.0: SC version 6.0 : 26/06/06## ############################################################### User: jzheng Run date: 7/12/2006 Run time: 10:47:58 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/lmb/jzheng/packages/ccp4-6.0.2 /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: new.pdb PDB file is being opened on unit 1 for INPUT. $WARNING: NO CRYST CARDS READ$ $WARNING: NO SCALE CARDS READ$ <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> $TEXT:Warning: $$ comment $$ WARNING: No Space group given on PDB CRYST1 line $$ <!--SUMMARY_END--></FONT></B> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> $TEXT:Warning: $$ comment $$ WARNING: NO CRYST CARDS READ FROM XYZIN $$ <!--SUMMARY_END--></FONT></B> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> $TEXT:Warning: $$ comment $$ WARNING: NO SCALE CARDS READ FROM XYZIN $$ <!--SUMMARY_END--></FONT></B> UNFORMATTED SCRATCH file opened on unit 7 <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> Logical name: SCTEMP, Filename: /tmp/jzheng/sc_tmp.14274 <!--SUMMARY_END--></FONT></B> Number of atoms read from PDB file: 3740 GRASP mode disabled - no Grasp output will be produced Selection commands: ------------------- Molecule 1 Number of atoms selected in chain A = 1870 Molecule 2 Number of atoms selected in chain B = 1870 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 1870 Number of atoms for second molecule 1870 Total number of atoms 3740 Setting up atoms for surfacing: Potential interface atoms 1446 Blocked atoms 2294 Atoms in Molecule 1 1870 Atoms in Molecule 2 1870 Output diagnostics from Connolly subroutine MDS: UNFORMATTED SCRATCH file opened on unit 7 <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> Logical name: SCDOTS, Filename: /tmp/jzheng/sc_dots.14274 <!--SUMMARY_END--></FONT></B> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> SC: imaginary contain SC: imaginary contain Times: User: 0.6s System: 0.1s Elapsed: 0:01 </pre> </html> <!--SUMMARY_END--></FONT></B>
