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. Cheers, Warren -- mailto:war...@sunesis.com 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:c...@cozzy.med.jhmi.edu] > Sent: Sunday, March 03, 2002 11:08 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] superimpose > > > Dear Sir, > > Does Pymol have the capability to superimpose molecules? If so how? > > Thanks, > > Michael > > 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 > > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
