Hi Mike, PyMOL has quite a few structure alignment and structure fitting options. If you want CE, check out CEalign on the PyMOLWiki (http://www.pymolwiki.org/index.php/Cealign). It's a script for PyMOL. I might build it into newer releases of PyMOL, if anyone's interested (let me know).
"align" performs a sequence alignment and then a structure superposition. After that, it goes through refinement cycles to improve the result. Align is fast and returns quality alignments for two sequences of high seq id. "super" does pairwise residue alignments followed by a superposition. It also does refinements to improve the overall quality. "optAlign," "fit" and others are just least square fitting routines once the atom correspondence is determined. Regards, -- Jason On Wed, Jan 27, 2010 at 5:55 PM, Michael Zimmermann <micha...@iastate.edu> wrote: > Dear PyMOL users, > > I have browsed the wiki and the first 300 mailing list messages in the > archive (the sourceforge archive does not seem to have a search set up > for the archive... arg!), but did not find any details about the > algorithms behind 'fit' and 'super.' I understand how align works, > and it sounds like fit is align but without the processing steps > (assumes 1:1 correspondence). Super, on the other hand, sounds more > like CE since it is sequence independent, but I cannot find any > corroboration on this. > > I want to run CE or a like algorithm (sequence independent - only > concerned with spacial arrangement of alpha carbons) on a large > dataset and want to know my options in terms of speed and accuracy. > > Sincerely, > Mike Z > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
