Hi everyone,
After SSM'ing a molecule in coot, when I open it in pymol, I end up with
molecules that don't make sense (such as a molecule that is enlarged by
a certain proportion, every bond has expanded by a certain proportion).
I realized that coot is overriding the CRYST1 card with the reference
molecule's symmetry information, but keeping SCALE cards for the moving
molecule. If I manually change the CRYST1 to match the original, or also
modify the SCALE to match the reference, pymol displays everything fine.
Unless I am missing something, SCALE cards store the transformation
matrix for converting orthogonal to fractional (crystallographic)
coordinates, and shouldn't coot stick to keeping the SCALE[1-3] and
CRYST1 cards together?
Engin
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Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
