I realized I made a mistake. The proper import statement is: from epymol import rigimol
This is shipped in the incentive build of 1.1r2. -- Jaso Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 2:50 PM, Huang, Xin <h...@amgen.com> wrote: > Thanks Jason. Does the latest version (1.2r2) of pymol comes with rigimol as > warren indicates on the website? I cannot seem to import rigimol. (I typed > "import rigimol" but have this import error "no module named rigimol). Any > suggestions? Many Thanks. > > > > -----Original Message----- > From: Jason Vertrees [mailto:jason.vertr...@gmail.com] > Sent: Friday, November 20, 2009 2:38 PM > To: Michael Zimmermann > Cc: Huang, Xin; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] make morph with rigimol > > 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
