From: Dirk K. <kos...@ge...> - 2009-09-01 13:17:01
|
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: kos...@ge... WWW: www.genzentrum.lmu.de ******************************************************* |
From: Schubert, C. [PRDUS] <CSC...@it...> - 2009-09-01 15:02:48
|
Dirk, you could try playing around with different transparency settings in subsequent scenes to emulate the effect. HTH Carsten From: Dirk Kostrewa [mailto:kos...@ge...] 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: kos...@ge... <mailto:kos...@lm...> WWW: www.genzentrum.lmu.de <mailto:kos...@lm...> ******************************************************* |
From: Dirk K. <kos...@ge...> - 2009-09-01 13:56:10
|
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:kos...@ge...] > 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: kos...@ge... > 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: kos...@ge... WWW: www.genzentrum.lmu.de ******************************************************* |
From: Schubert, C. [PRDUS] <CSC...@it...> - 2009-09-01 14:23:20
|
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 if you want to dive into python. Cheers, Carsten From: Dirk Kostrewa [mailto:kos...@ge...] 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:kos...@ge...] 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: kos...@ge... <mailto:kos...@lm...> WWW: www.genzentrum.lmu.de <mailto:kos...@lm...> ******************************************************* ******************************************************* 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: kos...@ge... <mailto:kos...@lm...> WWW: www.genzentrum.lmu.de <mailto:kos...@lm...> ******************************************************* |
From: Anastassis P. <a.p...@nk...> - 2009-09-01 14:32:51
|
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]" <CSC...@it... > 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:kos...@ge...] > 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:kos...@ge...] > 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: kos...@ge... > 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: kos...@ge... > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol- > us...@li... |
From: Matthew F. <Mat...@im...> - 2009-09-01 15:04:12
|
Hi Dirk - I would do this the basic way (because that's the only way I know). Write a PyMOL script - not a python script, just a series of PyMOL commands. Like this: (whatever commands you need to load and position your molecules and draw the surfaces) ray png movie_001.png set transparency=0.05, your_ligand ray png movie_002.png set transparency=0.1, your_ligand etc. Setting transparency to 1 is fully transparent, i.e. invisible. Transparency=0 is opaque. Once you've run this script, which you can invoke from the PyMOL command line by typing "run my_script", you'll have a series of image files showing the fade. I recommend using Quicktime Pro to fuse them into a movie - it only costs $30, and it's easy to use for this purpose. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 ________________________________ Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. |
From: Matthew D. H. <mh...@uv...> - 2009-09-01 15:18:16
|
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 <kos...@ge...>: > 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: kos...@ge... > WWW: www.genzentrum.lmu.de > ******************************************************* |
From: Tsjerk W. <ts...@gm...> - 2009-09-01 18:42:36
|
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. Hogg<mh...@uv...> 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 <kos...@ge...>: > >> 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: kos...@ge... >> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- 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 |
From: H. A. S. <ad...@st...> - 2009-09-01 19:46:55
|
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 _______________________________ |
From: Dirk K. <kos...@ge...> - 2009-09-02 09:10:04
|
Dear PyMOLers, thanks a lot to all of you for your helpful suggestions! I will try Tsjerk's way that probably keeps me from writing an external Fortran program for generating pymol commands ;-) Best regards, Dirk. Am 01.09.2009 um 20:42 schrieb Tsjerk Wassenaar: > 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. Hogg<mh...@uv...> 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 <kos...@ge...>: >> >>> 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: kos...@ge... >>> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol- > us...@li... ******************************************************* 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: kos...@ge... WWW: www.genzentrum.lmu.de ******************************************************* |