Colin, Unfortunately, that is hard to do: there is no guarantee that the proposed (characteristic) path of motion which relates any two spacial orientations will possess reasonable chemistry or sterics. RigiMOL does make an attempt to resolve simple conflicts, and the refinement step can address minor local violations, but that is about it.
The only way to work around this problem is to manually create one or more artificial intermediate conformations which do not exhibit such clashes and then morph conformation 1 to the first artificial conformation and then morph the last artificial conformation to conformation 2. That can be a lot of work, and it kind of misses the point: PyMOL (rigimol) structure morphs are only intended for visual comparison of two or more experimentally-determined structures. Molecular morphs are not (and should not be portrayed as) energetically-reasonable physiochemical paths of interconversion. To rigorously identify reasonable (low-energy) paths of interconversion, one must instead employ steered molecular dynamics or biased monte carlo simulations. Those are compute-intensive processes well beyond PyMOL's capabilities. Cheers, Warren > -----Original Message----- > From: Colin Levy [mailto:c.l...@manchester.ac.uk] > Sent: Thursday, September 10, 2009 8:59 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Rigimol > > Hi, > > I have generated a morph between two large scale domain motions using > Rigimol . The output is fine except that the two domains pass through > each other during their trajectory. Anyone know how to avoid this type > of problem. > > Thanks > > Colin > > ------------------------------------------------------------------------ -- > ---- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- > Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > 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 > > > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ 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
