From: Osvaldo M. <alo...@gm...> - 2012-02-01 14:26:01
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Hi all, I want to load several pdb files (between ~200) as frames (11 Megabytes), I want to be able to color by b-factor (each pdb file has diferent b-factor values) I use this code I take from http://www.pymolwiki.org/index.php/Load from glob import glob lst = glob("trj*.pdb") lst.sort()for fil in lst: cmd.load(fil,"mov", discrete=1) The problem is that when PyMOL is loading the first ~70 pdb/frames the loading process start to slow down quickly and then takes for ever to end loading the rest of the files (in fact I manually abort the session, because PyMOL virtually hangs). I am doing something wrong or is just that PyMOL is not really designed to load long trajectories (as for example VMD). There is someway to load all this files in an efficient way? A workaround is to load only the backbone of the protein (2,7 Megabytes). It takes one or two minutes to load everything. But I would prefer to have also the sidechains. I also try doing "cmd.hide()" just after loading each frame (I guess may be was some "overload" to display the molecules, but it did not help). Thanks. |
From: Jason V. <jas...@sc...> - 2012-02-01 14:41:53
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Hi Osvaldo, Try set defer_builds_mode, 5 then load your trajectories. Cheers, -- Jason On Wed, Feb 1, 2012 at 9:25 AM, Osvaldo Martin <alo...@gm...> wrote: > Hi all, > > I want to load several pdb files (between ~200) as frames (11 Megabytes), I > want to be able to color by b-factor (each pdb file has diferent b-factor > values) I use this code I take from http://www.pymolwiki.org/index.php/Load > > from glob import glob > lst = glob("trj*.pdb") > lst.sort() > for fil in lst: > cmd.load(fil,"mov", discrete=1) > > > > The problem is that when PyMOL is loading the first ~70 pdb/frames the > loading process start to slow down quickly and then > > > takes for ever to end loading the rest of the files (in fact I manually > abort the session, because PyMOL virtually hangs). > > I am doing something wrong or is just that PyMOL is not really designed to > load long trajectories (as for example VMD). > > > There is someway to load all this files in an efficient way? > A workaround is to load only the backbone of the protein (2,7 Megabytes). It > takes one or two minutes to load everything. > But I would prefer to have also the sidechains. I also try doing > "cmd.hide()" just after loading each frame > > > (I guess may be was some "overload" to display the molecules, but it did not > help). > > Thanks. > > > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |