Hi Dave, On Tue, 03 Feb 2009 16:33:28 -0500, David Garboczi <dgarbo...@niaid.nih.gov> wrote:
> I am examining packing in several space groups by issuing the command > > symexp foo, foo.pdb, sele, 10 > > If I select the whole reference molecule, I think that I should get > all the symmates within 10 A displayed. But for one of the crystals > that I am dealing with, > CRYST1 29.24 44.19 107.67 90.0 90.0 90.0 P 21 21 21 8 > > only four molecules are generated, the molecules are on top of one > another, and also are so far from each other that the packing can't > be real. The cell has 22% solvent. In Coot, however, this same > molecule and the "Cell & Symmetry" command gives rise to symmates > that look right and don't clash with each other. > > Help in figuring this out? I am using MacPyMol 1.1r1 on a ppc 10.4.11 Since you say that you are examining packing in several space groups (and so I'm guessing that maybe you have the same molecule in different space groups), I'm led to ask if you happened to move the molecule foo by aligning it to another molecule? This would cause the clash that you're seeing because PyMOL would be applying the symmetry operators to foo in the wrong position. 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 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
