hmm using TMalign method of superimposition I've solved that problem ( the atom order of ligand have been unchanged).
James 2013/2/7 James Starlight <jmsstarli...@gmail.com>: > Dear PyMol users! > > I've forced with the problem during superimposition of two identical > proteins. First of all I've defined in pymol > > set retain_order,1 > set pdb_retain_ids,1 > > to prevent changing of atom order after editing. > > than I do super system1, system2 > > and obtain changed atom order in system1 which have been moved ( in > particular in ligand's coordinates which are present in that system > but absent in the reference system2). > > > How I could fix it ? > > > James ------------------------------------------------------------------------------ Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb _______________________________________________ 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