RE: [PyMOL] Rtools Question
Hi Tony Friends, I just wanted to draw your attention to the fact that rTools should (in theory) work with the 0.95 OSX-X11 hybrid version, which has an native Aqua-based OpenGL window and an X11-based Tcl/Tk gui. I specifically created that version to insure that Mac users wouldn't be left unable to use external code such as this. PyMOLX11Hybrid is not quite as convenient as MacPyMOL since it requires a running instance of X11, but it is much easier to install than the Fink version of PyMOL and should provide the same compatibility. http://pymol.sourceforge.net/obtaining.html Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist 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 Tony Giannetti Sent: Friday, May 21, 2004 11:50 PM To: Olve Peersen Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Rtools Question Hey Olve, Not a prob, and since this is a common problem I will post my answer to the list. Kelley Moreman actually did a lot of this legwork so I give props to him. You are correct, the rTools that you can download from the web does not work on MacPyMol directly. Kelley was able to obtain an earlier version of the script that does work. I've attached it and it's called movie.py. Very simply, you put it in the same directory as the MacPyMol executable file (in the Mac system this is simply where the MacPyMol icon is located; you don't even have to open the archive. Once PyMol is loaded, type 'run movie.py' and everything is loaded. You can then input commands like mvSinrot and mvMov and all those great commands. Enclosed are other files from Kelley including more detailed setup instructions and a description of how the animation commands work. It's pretty easy once you get started. In about 2 days I constructed the movie for my thesis defense that can currently be viewed at: www.its.caltech.edu/~tonyg/smaller_fpnhyp.mov Of course moving objects independently of scene rotations isn't trivial, though it apparently can be done (Kelley and Warren have tips on this). For this movie, anything that moves was rendered with the rest of the scene objects turned off and then spliced into background scenes using photoshop scripts. Hope this helps you, and other Mac users. Tony On 5/21/04 11:12 PM, Olve Peersen olve.peer...@colostate.edu wrote: Tony, I was wondering if you could e-mail me or post the details of how you got rTools to work with MacPymol as opposed to X11 pymol for the Mac. I've fiddled with it a bit, but I cannot seem to get the movie commands to work. Thanks, Olve Peersen On May 15, 2004, at 11:25 PM, Tony Giannetti wrote: Hello all, This may have already been answered but I don't see it in the archives. I've got rTools working under MacPyMol and the effects are great. I'm working with a scene that has many objects loaded at once and I want to have some of them move independently over each other. So far I can only get rTools to apply rotations/translations to the whole scene, but not to individual objects. I can probably work around this using the alpha channel and then pasting the rendered images back onto the original scene in photoshop, but I'm wondering if there's a command scheme that will allow object one to rotate and translate according to rTools commands without altering the other objects in the scene. Thanks much, Tony --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- Olve Peersen Assistant Professor Dept. of Biochemistry Molecular Biology 1870 Campus Delivery Colorado State University Ft. Collins, CO 80523-1870 --- 970.491-0433Office 970.491-0271Lab 970.491-0494Fax ---
Re: [PyMOL] Rtools Question
Hey Olve, Not a prob, and since this is a common problem I will post my answer to the list. Kelley Moreman actually did a lot of this legwork so I give props to him. You are correct, the rTools that you can download from the web does not work on MacPyMol directly. Kelley was able to obtain an earlier version of the script that does work. I've attached it and it's called movie.py. Very simply, you put it in the same directory as the MacPyMol executable file (in the Mac system this is simply where the MacPyMol icon is located; you don't even have to open the archive. Once PyMol is loaded, type 'run movie.py' and everything is loaded. You can then input commands like mvSinrot and mvMov and all those great commands. Enclosed are other files from Kelley including more detailed setup instructions and a description of how the animation commands work. It's pretty easy once you get started. In about 2 days I constructed the movie for my thesis defense that can currently be viewed at: www.its.caltech.edu/~tonyg/smaller_fpnhyp.mov Of course moving objects independently of scene rotations isn't trivial, though it apparently can be done (Kelley and Warren have tips on this). For this movie, anything that moves was rendered with the rest of the scene objects turned off and then spliced into background scenes using photoshop scripts. Hope this helps you, and other Mac users. Tony On 5/21/04 11:12 PM, Olve Peersen olve.peer...@colostate.edu wrote: Tony, I was wondering if you could e-mail me or post the details of how you got rTools to work with MacPymol as opposed to X11 pymol for the Mac. I've fiddled with it a bit, but I cannot seem to get the movie commands to work. Thanks, Olve Peersen On May 15, 2004, at 11:25 PM, Tony Giannetti wrote: Hello all, This may have already been answered but I don't see it in the archives. I've got rTools working under MacPyMol and the effects are great. I'm working with a scene that has many objects loaded at once and I want to have some of them move independently over each other. So far I can only get rTools to apply rotations/translations to the whole scene, but not to individual objects. I can probably work around this using the alpha channel and then pasting the rendered images back onto the original scene in photoshop, but I'm wondering if there's a command scheme that will allow object one to rotate and translate according to rTools commands without altering the other objects in the scene. Thanks much, Tony --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- Olve Peersen Assistant Professor Dept. of Biochemistry Molecular Biology 1870 Campus Delivery Colorado State University Ft. Collins, CO 80523-1870 --- 970.491-0433Office 970.491-0271Lab 970.491-0494Fax --- Instructions - Read #135488.rtf Description: Binary data movie.py Description: Binary data AnimationCommands.txt Description: Binary data
Re: [PyMOL] Rtools Question
Dear Tony, You can get quite far with the mvCmd command. The parser will get confused if you issue complex commands that way, but there are workarounds. Example: You want to rotate one chain only over some movie frames. Step 1) write a rotate.pml script, containing: rotate x,5,chain A Step 2) use it from mvCmd: mvCmd 1-100,@rotate.pml movie For more complex things (like using the sin()-smoothed movement features), you will probably need to hack into rtools/rMovie.py Yours, Kristian Tony Giannetti wrote: Hello all, This may have already been answered but I don't see it in the archives. I've got rTools working under MacPyMol and the effects are great. I'm working with a scene that has many objects loaded at once and I want to have some of them move independently over each other. So far I can only get rTools to apply rotations/translations to the whole scene, but not to individual objects. I can probably work around this using the alpha channel and then pasting the rendered images back onto the original scene in photoshop, but I'm wondering if there's a command scheme that will allow object one to rotate and translate according to rTools commands without altering the other objects in the scene. Thanks much, Tony --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
