RE: [PyMOL] superimpose

[DeLano, W. <wa...@su...>]

Michael,

   The 'fit' command will do atom-for-atom RMS alignments, but all atom
attributes must match within each object (segment, chain, residue id,
residue name, atom name, etc.) for this to succeed.  As a result, the
'fit' command can be tricky to use.  Several 'alter' commands and a
'sort', are often needed to get the attributes to match before fitting.
'fit' only works for chemically identical models.

   PyMOL's fitting abilities are improving: the upcoming version (v0.80)
will have the ability to do an on-the-fly sequence-alignment followed by
an optimized structure alignment, saving considerable time and hassle. =20

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Michael S. Cosgrove [mailto:co...@co...]
> Sent: Sunday, March 03, 2002 11:08 AM
> To: pym...@li...
> Subject: [PyMOL] superimpose
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> Dear Sir,
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> Does Pymol have the capability to superimpose molecules? If so how?
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> Thanks,
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> Michael
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> Michael S. Cosgrove, Ph.D.
> Postdoctoral Fellow
> Johns Hopkins School of Medicine
> Department of Biophysics and Biophysical Chemistry
> 725 N. Wolfe Street, WBSB 603
> Baltimore MD, 21205
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> _______________________________________________
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