Hi Thomas, State handling in PyMOL has yet to come of age. In general, we need to do a better job at trajectories.
To answer your question, no you cannot easily just delete a state from a multistate protein. You can however, remap how PyMOL assigns states to frames, making your movie run more quickly. If you have 2000 states, played at one state per frame, at 20 FPS, that's 100 seconds of movie. You can shorten the movie with: # create 4 seconds of 30 FPS movie = 120 frames mset 1x120 # store frame 1 with object myTraj in state 1 mview store, 1, object=myTraj, state=1 # store frame 120 with object myTraj in state 2000 mview store, 120, object=myTraj, state=2000 mplay PyMOL will handle skipping states as necessary. Cheers, -- Jason On Fri, Oct 8, 2010 at 2:31 PM, Thomas Grant <tomer...@gmail.com> wrote: > Hi all, > > I've recently run a molecular dynamics simulation in Amber and have been > using PyMOL to create a simple movie of the trajectory. The smooth command > helps a lot with seeing the large motions I'm interested in. However, my > movie seems to run quite slow. Actually it runs quite fast, some 60 fps in > the PyMOL GUI, however it appears to run slow visually, i.e. motions take > more time than I'd like them to. Basically I would just like to speed up > the movie, but am limited by the fps of the output, and really have no need > for a 60 fps movie, 24 or 30 is quite fine. Ideally I'd like the movie to > take maybe five or ten seconds, but right now it takes nearly a minute, > since I have over 2000 states in my trajectory. > > My question is whether or not I can delete states, say every other state or > even more, without manually deleting each one, and end up with a seemingly > faster movie. I'm quite happy with 24 or 30 fps, since it's still perfectly > smooth to the eye. > > Is there some simple pymol command to do this? I've searched the wiki and > the archives and found a few similar feature requests from a few years ago, > but nothing as to whether or not this feature has been implemented. > > Any suggestions would be much appreciated! Thanks. > > Tom > > -- > Thomas D. Grant > Graduate Research Assistant > Hauptman-Woodward Medical Research Institute > 700 Ellicott St. > Buffalo, NY, USA 14203 > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ 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
