> Message: 4 > Date: Wed, 17 Jan 2007 09:21:26 -0800 (PST) > From: GAO FENG <mcf...@yahoo.com> > Subject: [PyMOL] How to superimpose two ligands? > To: pymol-users@lists.sourceforge.net > Message-ID: <621637.747...@web31110.mail.mud.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Everyone, > > Could someone tell me how to perform superimposition of two or more ligands > from different PDBs? > > Thanks in advance. > > Feng.
PyMolers, I'd like to follow up my previous post with a clarification. When Feng asked for superposition of ligands from two protein structures, I made the assumption that the residue pairings (sequence alignment) had already been completed for his ligands. Thus all that was needed was a translation and rotation of one set of coordinates onto the other; hence the suggestion to use optAlign from Kabsch. optAlign from the Kabsch code is a simply an algorithm to find the optimal superposition of two coordinate sets, nothing more. It does no pairings at all -- just rotate and translate. You have to find which residues to align to which other residues. One limitation on using CEAlign is that your selections must have more than 8 atoms. So, CEAlign could solve the problem entirely, but would need some modification to do so. Sorry if I confused anyone. References if needed: http://www.pymolwiki.org/index.php/Kabsch http://www.pymolwiki.org/index.php/Cealign Regards, -- Jason -- Jason Vertrees http://vertrees.org/ http://pymolwiki.org/ http://best.utmb.edu/
