[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] undisplaying residues
Bala, Switch the mode in which the mouse is selecting from residues to atoms. Then click the atom and do Hide-Everything. (To switch modes find the word Selecting in the lower right hand side of the screen, click it until Atoms shows up.) Now the mouse selects only atoms. Alternatively, I got just the DNA backbone to be visible (hiding all bases) by: # fetch and example PDB with DNA fetch 3gfi as cartoon zoom c. D # hide not the backbone hide everything, /N1 Hope this helps, -- Jason [PyMOL] undisplaying residues From: Bala subramanian bala.biophys...@gm... - 2009-08-31 07:00 Attachments: HTML-Email.html Friends, I made a cartoon representation of a DNA. now i want to undisplay the base and sugar of certain residues in the DNA. Could someone please write me how to do the same. When i select a residue and choose HIDE- EVERYTHING. It undisplays the cartoon of the backbone also which i dnt want. Regards, Bala -- Jason Vertrees, PhD PyMOL -- http://www.pymol.org/ PyMOLWiki -- http://www.pymolwiki.org/ -- 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] Inexplicable exception raised by cmd.color()
Stuart, I tried to replicate your problem. But, it worked as expected for me, so I'm thinking it might come down to your object names. Try this. Copy this into your PyMOL (or save it to a file and run it); does it work for you? # # color_example.py # # make 20 fake objects splay them out for x in range(20): cmd.pseudoatom( sym0 + str(x) + foo ) for x in range(20): cmd.translate( [2*x, 0, 0], sym0 + str(x) + foo) # change repr cmd.show_as(spheres) cmd.zoom(vis) # define colors colors = [ red, orange, yellow, green, blue, \ purple,salmon, grey, pink, teal, brown] # color them for i in range(len(colors)): cmd.color(colors[i],sym0+str(i)+*,quiet=0) It should show 20 spheres, where 11 are colored the same and rest brown. -- Jason [PyMOL] Inexplicable exception raised by cmd.color() From: Stuart Ballard srball...@wi... - 2009-08-26 23:32 Attachments: Message as HTML Hello Warren, all, When attempting to execute this block of code: colors = [red,orange,yellow,green,blue,purple,salmon,grey,pink,teal,brown] for i in range(10): cmd.color(colors[i], sym0 + str(i) + *) The following error message is displayed: Traceback (most recent call last): File /Users/delwarl/MacPyMOL090405/build/Deployment-py25/MacPyMOL.app/pymol/modules/pymol/parser.py, line 153, in parse File string, line 3, in module File /Users/delwarl/MacPyMOL090405/build/Deployment-py25/MacPyMOL.app/pymol/modules/pymol/viewing.py, line 2425, in color QuietException: pymol.parsing.QuietException instance at 0x104ea698 Furthermore, the object corresponding to sym00* is colored red, as expected. I've looked up the code in parser.py and viewing.py which generates the exception itself, and that has shed no light. Function color in viewing.py is as follows: # preprocess selection selection = selector.process(selection) color = _self._interpret_color(_self,str(color)) # r = DEFAULT_ERROR try: _self.lock(_self) r = _cmd.color(_self._COb,str(color),str(selection),int(flags),int(quiet)) finally: _self.unlock(r,_self) if _self._raising(r,_self): raise QuietException return r Any explanation of the bug, or an effective workaround would be greatly appreciated. Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- Jason Vertrees, PhD PyMOL -- http://www.pymol.org/ PyMOLWiki -- http://www.pymolwiki.org/ -- 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
[PyMOL] Showing Si and Re faces
Does anyone know how to show Re and Si faces of a backbone in PyMOL? I'm tired of putting them in by hand. The Re and SI faces of a backbone are the planes that can be drawn by connecting the alpha carbon to the carbonyl oxygen to the next alpha carbon to the hydrogen of the nitrogen back to the 1st alpha carbon. These planes are what make up the strands and the alpha helices when you show a protein as cartoon in PyMOL. Thanks in advance for any help! Adam -- ___ H. Adam Steinberg Designer, Artist, Scientist http://adam.steinbergs.us The Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 ___ -- 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
[PyMOL] Education
Hi folks, I'm using the latest version 1.2r1 of pymol for research etc and we have 0.99 in our lecture theatres (this is in the process of being upgraded to edu1_1 version - all windows. The problem is when I generate a nice presentation in 1.2r1 using align, surfaces etc it doesn't translate to the older versions. I can provide files if required Is the only option to generate educational presentations for my lectures using the edu version? Thanks J _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -- 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
[PyMOL] (no subject)
PS is it possible to run two versions at once on a PC (a quick test failed) _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -- 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
[PyMOL] broken
Hi again folks, Having tried to install both versions on my PC, then delete versions I can now only start pymol using the pymol.exe and any other automatic links bring the error: Error: Pymol failed to launch Aw Shucks I can get around this but it would be nice to restore to the original status quo. Thanks for any help J _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -- 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