Michael, Great advice. Also, I'd like to point out that the incentive build of PyMOL ships with the rigimol morphing module built in. Rigimol is only to be used for visualization, not for pathwway determination. If you only need to make a movie and don't necessarily care about a perfect pathway it's as easy as:
from pymol import rigimol load str1.pdb, str1 # load two structures load str2.pdb, str2 align str1, str2 # align them create m_in, str1, 1, 1 # create the input for rigimol create m_in, str2, 1, 2 rigimol.morph( "m_in", "m_out", refinement=5, async=1) This creates the "m_out" object as a multistate object. Save the output to a mutli-state PDB with: save myConf.pdb, m_out, 0 then use that in your movies. HTH, -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 2:08 PM, Michael Zimmermann <micha...@iastate.edu> wrote: > one option would be to make intermediates based on linear > interpolation and then make a movie of the "morph." Gerstein's group > has done some work at this. > http://www2.molmovdb.org/wiki/info/index.php/Morph_Server > > If you just want to visualize them together my suggestion would be to: > show one of the structures without the helix > make an object for the helix in each structure and another object with > both helices > show cartoons of each helix > show a transparent surface of the object with both helices > color each helix differently so that the cartoons and surfaces > represent conformational changes. > play with clipping planes applied to the transparent surface. > > you could do this type of image for the morph too to emphasize the helix. > > On Fri, Nov 20, 2009 at 12:45 PM, Huang, Xin <h...@amgen.com> wrote: >> I want to make movie showing conformational changes of one helix (including >> a couple of side chains) between two structures of the same protein. Could >> anybody teach me how to make morph using pymol version 1.2r2? >> >> Many Thanks. >> >> ------------------------------------------------------------------------------ >> 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 > ------------------------------------------------------------------------------ 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
