[PyMOL] pymol autodock plugin
Dear PyMOLers, there is a new version of the plugin on the web (http://wwwuser.gwdg.de/~dseelig/adplugin.html). It contains a bunch of new features, like: - setup and execution of complete docking runs - support for VINA (http://vina.scripps.edu), a great new Autodock spawn - viewing of Autodock grid maps in PyMOL - some lightweight virtual screening functionality So far it's only tested on Linux and by myself so I expect it to be somewhat buggy and unstable. Therefore please report bugs. Cheers, Daniel On Thursday 13 August 2009 22:36:14 Warren DeLano wrote: Jed, With the 1.2 release of PyMOL, we have completely switched over to Numpy. So the first thing to try is to replace: from Numeric import * # with from numpy import * Cheers, Warren -Original Message- From: Jed Goldstone [mailto:jedg...@mit.edu] Sent: Thursday, August 13, 2009 1:34 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol autodock plugin The autodock plugin written by Daniel Seeliger ceased to function (load) when I upgraded to Pymol 1.2r1. Although it is not compatible directly with Autodock 4, it did have the useful functionality of presenting an autodock 'box' that was readily tweakable, so that the parameters could be exported for Autodock Vina. I would LOVE to have this resurrected, but I don't know python - can anybody help with this? The specific failures I got were: File C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py, line 16, in module from Numeric import * ImportError: No module named Numeric Error: unable to initialize plugin 'autodock'. Any help would be greatly appreciated. Jed -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.mit.edu/people/jedgold/home.html (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) -- 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 -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen, Germany Tel: +49 551 201 2310 Fax: +49 551 201 2302 email: dsee...@gwdg.de web: http://wwwuser.gwdg.de/~dseelig -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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
[PyMOL] movie.roll in middle of movie
Good afternoon all - I think I have a simple question. I would like to have a series of zooms followed by a movie.roll and then zooming back to the start position. Here is what I have cmd.mset(1 x800) cmd.zoom(center,200) cmd.frame(1) cmd.mview(store) cmd.zoom(center,50) cmd.frame(120) cmd.mview(store) cmd.frame(180) cmd.mview(store) cmd.zoom(center,15) cmd.frame(280) cmd.mview(store) cmd.frame(360) cmd.mview(store) cmd.zoom(center,50) cmd.frame(400) cmd.mview(store) cmd.frame(420) cmd.mview(store) cmd.movie.roll(421,755) cmd.mview(store) cmd.frame(756) cmd.mview(store) cmd.zoom(center,200) cmd.frame(800) cmd.mview(reinterpolate) The problem is that is does not do the movie.roll and as the movie plays over and over it actually performs all the zoom actions and then rotates one frame and then starts the process again from that newly rotated frame. I would like it to perform the full rotation after the initial zoom and then perform the final zoom command. Any ideas where I might have messed this up? Many thanks Ben -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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
Re: [PyMOL] movie.roll in middle of movie
Note that this kind of stuff is much easier in PyMOL 1.2 without any scripting. (ScreenCasts for PyMOL Sponsors at http://delsci.info/id/media:new12 under Complex Movie Creation -- login first). Nevertheless, a possible answer is below: Cheers, Warren # PyMOL .pml file (tested against PyMOL 1.2) load $PYMOL_PATH/test/dat/1tii.pdb unset movie_auto_interpolate unset movie_loop mset 1 x800 zoom center,200 frame 1 mview store zoom center,50 frame 120 mview store frame 180 mview store zoom center,15 frame 280 mview store frame 360 mview store zoom center,50 frame 400 mview store frame 420 mview store mview interpolate # instead of: movie.roll 421,755 frame 531 turn y,120 mview store frame 642 turn y,120 mview store frame 756 turn y,120 mview store mview interpolate, power=1 zoom center,200 frame 800 set movie_loop mview interpolate mview smooth mplay -Original Message- From: Benjamin Bobay [mailto:ben.bo...@gmail.com] Sent: Wednesday, September 16, 2009 8:41 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] movie.roll in middle of movie Good afternoon all - I think I have a simple question. I would like to have a series of zooms followed by a movie.roll and then zooming back to the start position. Here is what I have cmd.mset(1 x800) cmd.zoom(center,200) cmd.frame(1) cmd.mview(store) cmd.zoom(center,50) cmd.frame(120) cmd.mview(store) cmd.frame(180) cmd.mview(store) cmd.zoom(center,15) cmd.frame(280) cmd.mview(store) cmd.frame(360) cmd.mview(store) cmd.zoom(center,50) cmd.frame(400) cmd.mview(store) cmd.frame(420) cmd.mview(store) cmd.movie.roll(421,755) cmd.mview(store) cmd.frame(756) cmd.mview(store) cmd.zoom(center,200) cmd.frame(800) cmd.mview(reinterpolate) The problem is that is does not do the movie.roll and as the movie plays over and over it actually performs all the zoom actions and then rotates one frame and then starts the process again from that newly rotated frame. I would like it to perform the full rotation after the initial zoom and then perform the final zoom command. Any ideas where I might have messed this up? Many thanks Ben -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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
