[PyMOL] Smooth fading of surface in movie?
Dear Warren, using PyMOL without any additional plug-ins, like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- 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
Re: [PyMOL] Smooth fading of surface in movie?
Dear Carsten, yes, thanks. However, for a smooth fading, that would require a lot of scenes. Is there a simple python loop, that would create scenes with smooth transparency fading-in from 0 to 1 and that I could use in my pymol-scripts? Unfortunately, I'm not familiar with python, yet ... Best regards, Dirk. Am 01.09.2009 um 15:39 schrieb Schubert, Carsten [PRDUS]: Dirk, you could try playing around with different transparency settings in subsequent scenes to emulate the effect. HTH Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, September 01, 2009 8:57 AM To: PyMOLBB Subject: [PyMOL] Smooth fading of surface in movie? Dear Warren, using PyMOL without any additional plug-ins, like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- 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
Re: [PyMOL] Smooth fading of surface in movie?
A silly but working solution is to embed the pymol script in a csh script which changes the value for the transparency in small steps. Not ellegant but if you know csh/sh/bash it's easy. A. Sent from my iPhone On 1 Sep 2009, at 16:23, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: That would require execution of a python program within a specific scene, which is not supported as far as I know. Scenes are intended to be static representations of display states, for lack of a better word. You would need to manually run the fade script before transitioning the scene. Not sure if this is what you want. Looks as if you may be better off plunging into movies if you really need the effect. Mark Lutz, David Asher , Learning Python, o’Reilly Great book i f you want to dive into python. Cheers, Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, September 01, 2009 9:56 AM To: PyMOLBB Subject: Re: [PyMOL] Smooth fading of surface in movie? Dear Carsten, yes, thanks. However, for a smooth fading, that would require a lot of scenes. Is there a simple python loop, that would create scenes with smooth transparency fading-in from 0 to 1 and that I could use in my pymol-scripts? Unfortunately, I'm not familiar with python, yet ... Best regards, Dirk. Am 01.09.2009 um 15:39 schrieb Schubert, Carsten [PRDUS]: Dirk, you could try playing around with different transparency settings in subsequent scenes to emulate the effect. HTH Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, September 01, 2009 8:57 AM To: PyMOLBB Subject: [PyMOL] Smooth fading of surface in movie? Dear Warren, using PyMOL without any additional plug-ins, like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** --- --- --- - 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- us...@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
Re: [PyMOL] Smooth fading of surface in movie?
Dirk, you could try playing around with different transparency settings in subsequent scenes to emulate the effect. HTH Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, September 01, 2009 8:57 AM To: PyMOLBB Subject: [PyMOL] Smooth fading of surface in movie? Dear Warren, using PyMOL without any additional plug-ins, like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail:kostr...@genzentrum.lmu.de mailto:kostr...@lmb.uni-muenchen.de WWW:www.genzentrum.lmu.de mailto:kostr...@lmb.uni-muenchen.de *** -- 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
Re: [PyMOL] Smooth fading of surface in movie?
I use a clunky set of mdo commands to do this. mdo 266: set transparency, .1, (palm+linker+Nterm) mdo 267: set transparency, .2, (palm+linker+Nterm) mdo 268: set transparency, .3, (palm+linker+Nterm) mdo 269: set transparency, .4, (palm+linker+Nterm) mdo 270: set transparency, .5, (palm+linker+Nterm) mdo 271: set transparency, .6, (palm+linker+Nterm) mdo 272: set transparency, .7, (palm+linker+Nterm) mdo 273: set transparency, .8, (palm+linker+Nterm) mdo 274: set transparency, .9, (palm+linker+Nterm) mdo 275: set transparency, 1, (palm+linker+Nterm) If the surfaces are turned on for objects palm, linker and Nterm, then this will fade out the surface over frames 266 to 275. Setting the transparency to 1 and then reversing the order of the values will make the surface fade in. HTH Matthew Hogg University of Vermont Burlington, VT 05405 Quoting Dirk Kostrewa kostr...@genzentrum.lmu.de: Dear Warren, using PyMOL without any additional plug-ins, like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone:+49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW: www.genzentrum.lmu.de *** -- 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
Re: [PyMOL] Smooth fading of surface in movie?
Hi :) Some people are just not lazy enough ;) Lazy people like me spend a good deal of effort thinking about how to avoid efforts like writing repetitive lines :p And then you could come up with: from math import sin,pi mset 1 x300 for i in range(200,301): cmd.mdo( i, set transparency,selection,%f % ( math.sin( math.pi*(i-200)/(2*100) ) ) ) The fuzz with the sine is of course to have a smoother fade. One could also take the simpler linear fade, but mind that the either numerator or divisor (or both) have to be float in order to end up with a float: for i in range(200,301): cmd.mdo( i, set transparency,selection,%f % ( (i-200)/100.0 ) ) With a bit more scripting, you can easily use this to define functions for fading properties from one value to another over a given range of frames. As a side note, if the fade is part of a more complex movie, hide the surface one frame after the fade has completed. Possibly it's also best to explicitly show it again in the first frame, in case you have Pymol cycle through the movie. In case the purpose is fading in the surface, start with surface view hidden and turn on the surface the frame before you start the fade. This way you avoid Pymol calculating its way through a null surface, possibly even coming up with some artefacts... Hope it helps, Tsjerk On Tue, Sep 1, 2009 at 5:01 PM, Matthew D. Hoggmh...@uvm.edu wrote: I use a clunky set of mdo commands to do this. mdo 266: set transparency, .1, (palm+linker+Nterm) mdo 267: set transparency, .2, (palm+linker+Nterm) mdo 268: set transparency, .3, (palm+linker+Nterm) mdo 269: set transparency, .4, (palm+linker+Nterm) mdo 270: set transparency, .5, (palm+linker+Nterm) mdo 271: set transparency, .6, (palm+linker+Nterm) mdo 272: set transparency, .7, (palm+linker+Nterm) mdo 273: set transparency, .8, (palm+linker+Nterm) mdo 274: set transparency, .9, (palm+linker+Nterm) mdo 275: set transparency, 1, (palm+linker+Nterm) If the surfaces are turned on for objects palm, linker and Nterm, then this will fade out the surface over frames 266 to 275. Setting the transparency to 1 and then reversing the order of the values will make the surface fade in. HTH Matthew Hogg University of Vermont Burlington, VT 05405 Quoting Dirk Kostrewa kostr...@genzentrum.lmu.de: Dear Warren, using PyMOL without any additional plug-ins, like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW: www.genzentrum.lmu.de *** -- 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- 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
