Carlo, If B is the chain ID for the matched seguments, then it should be as simple as:
load file1.pdb load file2.pdb align file1//B//CA, file2//B//CA Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Carlo Zambonelli > Sent: Thursday, March 20, 2008 11:37 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] partial alignment (super?) > > Hi, > I have 2 pdb files corresponding to 2 partially overlapping proteins: > AB' and B"C. B' and B" have similar but not identical > structures. I want to align B' and B" so to obtain ABC. Can I > select to align only portions of molecules? Another > possibility is to create 2 new pdb files corresponding to B' > and B", do the alignment and then attach back A and C, even > though I'm not completely sure after importing A and C in the > B'-B" alignment session, how I would correctly position A and > C with their original orientations relative to B' and B". > Thank you for your help! > Carlo > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft Defy all > challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
