From: Dirk K. <dir...@ps...> - 2005-09-26 07:49:52
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Hi Warren, the scenes feature in PyMOL is _really_ nice! By choosing appropriate scenes, it does exactly what I would like to show in a movie describing a protein structure. Is there a way in PyMOL to export the individual frames for a movie from scenes? If not, this would be my most desired missing feature in PyMOL! Best regards, Dirk. -- **************************************** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail: dir...@ps... http://sb.web.psi.ch **************************************** |
From: <an...@bi...> - 2005-09-26 08:16:55
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Dirk is right. Scenes are way nice. What I am wondering is if there is = a way of incorporating them into powerpoint a little more smoothly than I currently do. As has been suggested by many, I use a hyperlink to the .psw file. Under XP, this fires up pymol, even if pymol is already running in the background. In other words, for a second or so, I see the empty pymol window on top of the current slide of my presentation as pymol is starting. Is there a way to open the session with pymol that is already running? Under OSX, the session file is opened in a running pymol session (pymolX11Hybrid), but the transition is even rougher than under XP. The current slide disappears and the Mac contemplates for a while before opening the session. The G5 is much slower than my XP notebook, but are there any tricks to smoothen things up? Has anyone tried this with StarOffice under linux? Thanks Andreas > Hi Warren, > > the scenes feature in PyMOL is _really_ nice! By choosing appropriate > scenes, it does exactly what I would like to show in a movie describing > a protein structure. Is there a way in PyMOL to export the individual > frames for a movie from scenes? If not, this would be my most desired > missing feature in PyMOL! > > Best regards, > > Dirk. > --=20 --> Andreas F=F6rster <-- 8 rue Doudart de Lagr=E9e, 38000 Grenoble ++33.(0)438.866201 and ++33.(0)456.452000 www.biochem.utah.edu/~andreas |
From: Peter A. M. <pa...@co...> - 2005-09-26 21:22:20
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Hi Dirk, > a protein structure. Is there a way in PyMOL to export the individual frames for a movie from scenes? If not, this would be my most desired missing feature in PyMOL! Yes. What I do is to use a script to step through each frame of the movie (rotation by 1 degree, zoom in slightly, change transparency slightly, etc), ray-trace (optional), and dump the png. From there, ffmpeg will combine all of these into a single movie file (memcoder is supposed to do this as well). I'm not entirely sure what you mean by frames from scenes, though. Hope this helps, Pete Pete Meyer Fu Lab BMCB grad student Cornell University |
From: Martin N. <ne...@xr...> - 2005-09-27 09:07:38
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Dirk, Actually there is a way to render a movie from predefined scenes. I created a .pse-file with my desired scenes and then made a movie from the extrapolations between the scenes. It will look pretty much as an ordinary scene_animation in Pymol. From the movie I rendered lots of .png-files which I finally merged into a .mpg or .avi movie. It's time consuming but it works. Here is a sample script that will render a 50 frame movie from two scenes stored in movie.pse: ********************************'' load movie.pse set scene_animation,-1 set scene_animation_duration,0 mset 1 x50 scene F1 mview store, 1 scene F2 mview store, 30 mview store, 35 scene F1 mview store, 50 mview interpolate set ray_trace_frames = 1 mpng movie ********************************'' Hope this is to some help. cheers /Martin At 09:49 2005-09-26, Dirk Kostrewa wrote: >Hi Warren, > >the scenes feature in PyMOL is _really_ nice! By choosing appropriate >scenes, it does exactly what I would like to show in a movie describing a >protein structure. Is there a way in PyMOL to export the individual frames >for a movie from scenes? If not, this would be my most desired missing >feature in PyMOL! > >Best regards, > >Dirk. > >-- > >**************************************** >Dirk Kostrewa >Paul Scherrer Institut >Life Sciences, OFLC/110 >CH-5232 Villigen PSI, Switzerland >Phone: +41-56-310-4722 >Fax: +41-56-310-5288 >E-mail: dir...@ps... >http://sb.web.psi.ch >**************************************** > > > >------------------------------------------------------- >SF.Net email is sponsored by: >Tame your development challenges with Apache's Geronimo App Server. >Download it for free - -and be entered to win a 42" plasma tv or your very >own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users ____________________________________ Martin Nervall Molecular Biotechnology Program Dept. of Cell & Molecular Biology Biomedical Center Box 596 SE-751 24 Uppsala Sweden Phone +46 (0)18 471 5058 http://xray.bmc.uu.se/~aqwww/ |
From: Dirk K. <dir...@ps...> - 2005-09-27 14:11:39
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Hi Martin, your script works beautifully!!! Thank you very much!!! I would like to understand two commands that you use in your script, for which I couldn't find any infos, neither in the manual, nor in the reference nor in the WiKi. Could you please tell me: - what does "set scene_animation,-1" mean? - what do the "mview store" and "mview interpolate" commands mean? Thanks again!!! Best regards, Dirk. Martin Nervall wrote: > Dirk, > > Actually there is a way to render a movie from predefined scenes. I > created a .pse-file with my desired scenes and then made a movie from > the extrapolations between the scenes. It will look pretty much as an > ordinary scene_animation in Pymol. From the movie I rendered lots of > .png-files which I finally merged into a .mpg or .avi movie. It's time > consuming but it works. > > Here is a sample script that will render a 50 frame movie from two > scenes stored in movie.pse: > > ********************************'' > load movie.pse > set scene_animation,-1 > set scene_animation_duration,0 > > mset 1 x50 > scene F1 > mview store, 1 > > scene F2 > mview store, 30 > mview store, 35 > > scene F1 > mview store, 50 > > mview interpolate > > set ray_trace_frames = 1 > mpng movie > ********************************'' > > Hope this is to some help. > > cheers > > /Martin > > At 09:49 2005-09-26, Dirk Kostrewa wrote: > >> Hi Warren, >> >> the scenes feature in PyMOL is _really_ nice! By choosing appropriate >> scenes, it does exactly what I would like to show in a movie >> describing a protein structure. Is there a way in PyMOL to export the >> individual frames for a movie from scenes? If not, this would be my >> most desired missing feature in PyMOL! >> >> Best regards, >> >> Dirk. >> >> -- >> >> **************************************** >> Dirk Kostrewa >> Paul Scherrer Institut >> Life Sciences, OFLC/110 >> CH-5232 Villigen PSI, Switzerland >> Phone: +41-56-310-4722 >> Fax: +41-56-310-5288 >> E-mail: dir...@ps... >> http://sb.web.psi.ch >> **************************************** >> >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: >> Tame your development challenges with Apache's Geronimo App Server. >> Download it for free - -and be entered to win a 42" plasma tv or your >> very >> own Sony(tm)PSP. Click here to play: >> http://sourceforge.net/geronimo.php >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > ____________________________________ > Martin Nervall > Molecular Biotechnology Program > Dept. of Cell & Molecular Biology > Biomedical Center > Box 596 > SE-751 24 Uppsala > Sweden > Phone +46 (0)18 471 5058 > http://xray.bmc.uu.se/~aqwww/ > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download it for free - -and be entered to win a 42" plasma tv or your > very > own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users -- **************************************** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail: dir...@ps... http://sb.web.psi.ch **************************************** |