Dear Jae, On Thu, 23 Oct 2008 17:05:32 +0100, Jae Hyun <[EMAIL PROTECTED]> wrote:
> I tried to calculate the shape complementarity parameter using Sc in CCP4. > But, this gave me error message as follows: > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > > $TEXT:Warning: $$ comment $$ > WARNING: No Space group given on PDB CRYST1 line > $$ > <!--SUMMARY_END--></FONT></B> This is just a warning. The real error is below. > UNFORMATTED SCRATCH file opened on unit 7 > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > Logical name: SCTEMP, Filename: /tmp/jhbae/sc_tmp.02978 > <!--SUMMARY_END--></FONT></B> > > > Number of atoms read from PDB file: 4144 > > > GRASP mode disabled - no Grasp output will be produced > > Selection commands: > ------------------- > > Molecule 1 > Number of atoms selected in chain A = 2372 > > Molecule 2 > Number of atoms selected in chain B = 1772 > > 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 : .50 per square Angstrom > No radius found for > Residue PTR Atom CG ^^^^^^^^^^^^^^^^ This is the real error. You have an atom called "CG" in a residue called "PTR" which does not exist in the radii file. You can copy the radii file and add your own entries to it and use that with the command line option: SCRADII radii.lib Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <[EMAIL PROTECTED]> http://pldserver1.biochem.queensu.ca/~rlc
