Yunbo, > Can I use pymol to superimpose two protein structures ? How > should I do?
You want the align command. Example usage with 2 pdb files: load prot1.pdb load prot2.pdb align prot1////ca, prot2////ca It may be necessary to restrict the alignment region to certain chains. For example, to match chain A to chain B: align prot1//A//ca, prot2//B//ca Cheers, Warren (PS. thanks for responding Jennifer!) -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > yunbo.song > Sent: Thursday, May 05, 2005 11:18 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] the conserved residues can be overlapped? > > Ok, thanks. But, its not what I meant. I want to let 2 > proteins automatically overlap according to the amino acid > sequence alignment,i.e. the conserved residues can be > overlapped. Can I do it use pymol or any other program? > > thanks > May 5 > > > > hi, > > I had a similar question, and here is the answer. > > Jennifer, > > Yes.?Switch the mouse into "3 button editing mode", and then > shift-left-click-and-drag to rotate and > shift-middle-click-and-drag to translate. > > Cheers, > Warren > > I found that this approach works best if you are in stick or > line mode. > I hope this helps. > > -Jennifer Pfingsten > (UCHSC) > > > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net on behalf of yunbo.song > Sent: Thu 5/5/2005 11:56 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] can superimpose two protein structures ? > > Hi, all, > > Can I use pymol to superimpose two protein structures ? How > should I do? > If it cannot, anybody can tell me what program can do > superposition very easily? thanks! > > May 5 > > >
