Feng, Kabsch can do this, possibly. I just tested two proteins (1cll and 1ggz) which both have 4 calciums at very similar locations:
PyMOL> load 1cll.pdb PyMOL> load 1ggz.pdb PyMOL> optAlign 1cll and e. CA, 1GGZ and e. CA RMSD=2.254852 You could try that. Kabsch (and optAlign) can be found on the wiki (http://www.pymolwiki.org/index.php/Kabsch#The_New_Code). I suggest you grab the New Code if this works for you. Cheers, -- Jason On Wednesday 17 January 2007 11:21, pymol-users-requ...@lists.sourceforge.net wrote: > 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. -- Jason Vertrees (javer...@utmb.edu) http://vertrees.org/ -- HOME http://pymolwiki.org/ -- PyMol Wiki http://best.utmb.edu/ -- Protein Science http://www.andeanimporters.com/ -- Biz.
