Kelley, Thanks for drawing these issues to our attention. Kristian and I haven't yet really had a chance to figure out how to integrate his stuff into the main version most effectively, but the fault has been entirely mine though, since my day job at Sunesis dominated my schedule to such a great extent.
Thanks to sponsorship from your group and others, I have now been able to clear my schedule to work on PyMOL full-time (albeit with a massive pay cut), so this area and many other areas should start to get much-needed attention. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Kelley Moremen Sent: Tuesday, April 01, 2003 6:12 AM To: Kristian Rother; pymol-users@lists.sourceforge.net; war...@delanoscientific.com Subject: Re: [PyMOL] Movement in animations: version 2 Dear Kristian, Warren, and other Pymolers: In regard to my previously stated problems in making movement animations in Pymol, I have tried the rTools plug-in before, and I tried it again after your suggestion. In my system they do not work correctly, or at least I have not installed them correctly. I am running both a Mac powerbook and a G4 desktop machine, with either the stand-alone Pymol 10.2 for Mac OSX or Pymol version 0.86 running in unix in the Mac X11 version of the X windows system. As indicated in the install instructions for rTools (version0.5.2) I have copied the rubor.py and rubor/ directory into the .../modules/pmg_tk/startup directory, modified the path in rConfig.py, created /tmp and /pdb directories (in the startup directory because the install instructions were not clear on this topic), added the relevant lines to PMGApp.py. I should state that several aspects of the install instructions in regard to the directory structures in my system were unclear. In both versions of Pymol described above, when a simple move command is inserted into a script as follows: mset 1 x100 mvMove 20-40,x,80 movie I get the following error messages: PyMOL>mset 1 x100 PyMOL>mvMove 20-40,x,80 Traceback (most recent call last): File "/Applications/PyMOL/Darwin/modules/pymol/parser.py", line 234, in pars e exec(com2[nest],pymol_names,pymol_names) File "<string>", line 1 mvMove 20-40,x,80 ^ SyntaxError: invalid syntax PyMOL>movie Error: ambiguous command: movie.load movie.rock movie.screw movie.zoom movie.nutate movie.roll movie.tdroll Obviously I have made a mistake in the install process somewhere, and I would appreciate a more detailed description of where and why the plug-in components are supposed to be inserted since I will have to interpret them for my own directory structure rather than a standard Linux install. Regardless of all of the above, there also MUST be an easier way to do the animations that I need. Is there no direct scripting in Pymol that can do the equivalent smooth moves or transitions? The rTools package may be the way to go in the future, especially if it in incorporated in a seemless manner into the next version of Pymol that works in ALL platforms without undue tinkering with scripts and directory structures. In the meantime is there an effective Pymol scripting approach that will work in the platforms that I have described above? Any assistance would be greatly appreciated. Regards, Kelley On 4/1/03 4:43 AM, "Kristian Rother" <kristian.rot...@charite.de> wrote: > Am Montag, 31. März 2003 23:18 schrieb Kelley Moremen: >> Dear Pymolers: >> >> The problem comes when I want to make defined rolls, zooms, or moves that >> start and stop at specific places. There must be a better way than >> concatenating a collection of "move x,10" commands. I have seen in several > > There is a plug-in for PyMOL on http://www.rubor.de/bioinf/ that has been > designed to handle that kind of thing. With it installed, you can do the > following: > > mvMove 1-100,z,50 # Zoom over frames 1-100 > mvRot 50-110,x,260 # Rotate around x-axis > mvSet 1-10,transparency,1.0,0.0 # fade surface in > movie # start the whole thing > > Maybe that helps, > > Kristian Rother > Dr. Kelley Moremen Associate Professor Complex Carbohydrate Research Center Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602-7229 Office (706) 542-1705 Fax: (706) 542-1759 Email: more...@arches.uga.edu (send email with large attachments to: more...@bmb.uga.edu) Website: http://bmbiris.bmb.uga.edu/moremen/lab/ ------------------------------------------------------- This SF.net email is sponsored by: ValueWeb: Dedicated Hosting for just $79/mo with 500 GB of bandwidth! No other company gives more support or power for your dedicated server http://click.atdmt.com/AFF/go/sdnxxaff00300020aff/direct/01/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
