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pdbsubmission macro discrepancies?

malhota malhota at rockvax.rockefeller.edu
Mon Dec 9 18:26:15 EST 1996

I am using xplor 3.851 to prepare a pdb file for submission (using the
macro pdbsubmission, and the example pdb_submit.inp files). I see a
small difference in the RMS deviations in bonds, angles, torsions and
so on as reported using the macro, and when these values are calculated
using the "print threshold" statement in a xplor run, even though the
macro also uses the "print threshold" statement to compute these

The differences are small (0.014 using the macro vs 0.012 otherwise for
RMS bond deviations; 1.71117 vs 1.637 for RMS angle deviations, and so
on). The atoms selected, psf, topology, and paramater files are all the
same in each case. The numbers computed without the macro also agree
with xplor 3.1 results (the model was refined using xplor 3.1).

Does the macro do these calculations differently ?

By the way, the pdbsubmission macro is a wonderful resource for pdb
file preparation!

Arun Malhotra                 Phone: (212) 327-7478
1230 York Avenue, Box 224       fax: (212) 327-7477
The Rockefeller University
New York, NY 10021         Internet: malhota at rockvax.rockefeller.edu

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