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 21 218
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: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
