[PyMOL] object-specific Z-clipping
Dear all, Does anyone know whether object-selective z-clipping has been implemented in the newer Pymol version(s)? If not, has anyone found any solution around (since 2002 no new threads on the matter)? Thanks, Shura Mankin -- Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] form and break bonds in movie
Hi there, First post here, so hello to everybody! I would like to produce a movie where covalent bonds break and form. However, when I load the .pdb files in PyMOL and play a movie, the bond status (formed or broken) stays the same as seen on the first state, even if bond lenghts change considerably. Any tips on how to do this are welcome. I have googled and searched the archives, but found nothing. Greetings, G -- Guilherme Menegon Arantes, PhD São Paulo, Brasil __ -- Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] form and break bonds in movie
Hi there, I would like to produce a movie where bonds break and form. However, when I load the .pdb files in PyMOL, the bond status (formed or broken) stays the same as seen for the first state, even if the bond lenghts change considerably. Any tips on how to do this are welcome. I have goggled and searched the archives, but found nothing. Greetings, G -- Guilherme Menegon Arantes, PhD São Paulo, Brasil __ -- Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] form and break bonds in movie
Whoops, my bad -- I duped the approval before seeing your repost!
Answer:
# first create a phony molecular trajectory
load $PYMOL_PATH/test/dat/pept.pdb, obj
for a in range(2,31): cmd.create("obj","obj",1,a)
unbond 5/c, 6/n
protect not ((5/c or 6/n) extend 4)
sculpt_activate obj, 30
sculpt_iterate obj, 30, 100
smooth obj, 30, 3
# then program a bond-break/re-form movie
mset 1 x30 1 -30 30 x30 30 -1
mdo 45: unbond 5/c, 6/n, quiet=1
mdo 100: bond 5/c, 6/n, quiet=1
frame 100
as sticks
orient 5-6/n+ca+c
mplay
# NOTE: only tested on PyMOL 1.2.x
Cheers,
warren
> -Original Message-
> From: Guilherme Menegon Arantes [mailto:garan...@iq.usp.br]
> Sent: Wednesday, April 29, 2009 6:44 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] form and break bonds in movie
>
>
> Hi there,
>
> I would like to produce a movie where bonds break and form. However,
> when I load the .pdb files in PyMOL, the bond status (formed or broken)
> stays the same as seen for the first state, even if the bond
> lenghts change considerably.
>
> Any tips on how to do this are welcome. I have goggled and searched the
> archives, but found nothing.
>
> Greetings,
>
> G
>
> --
>
> Guilherme Menegon Arantes, PhD São Paulo, Brasil
> __
>
>
> --
>
> Register Now & Save for Velocity, the Web Performance & Operations
> Conference from O'Reilly Media. Velocity features a full day of
> expert-led, hands-on workshops and two days of sessions from industry
> leaders in dedicated Performance & Operations tracks. Use code vel09scf
> and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
--
Register Now & Save for Velocity, the Web Performance & Operations
Conference from O'Reilly Media. Velocity features a full day of
expert-led, hands-on workshops and two days of sessions from industry
leaders in dedicated Performance & Operations tracks. Use code vel09scf
and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
___
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Re: [PyMOL] object-specific Z-clipping
Sorry, still not done (I have made two attempts, but both failed). While OpenGL supports arbitrary clipping planes, accomplishing this correctly in the ray tracer is a much harder problem that one might think... Cheers, Warren > -Original Message- > From: Mankin Alexander [mailto:sh...@uic.edu] > Sent: Wednesday, April 29, 2009 6:18 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] object-specific Z-clipping > > Dear all, > Does anyone know whether object-selective z-clipping has been > implemented in the newer Pymol version(s)? If not, has anyone found > any solution around (since 2002 no new threads on the matter)? > Thanks, > Shura Mankin > -- Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] object-specific Z-clipping
BS"D There is a workaround to this problem, which I used in a different program and have suggested in the past to Warren and others. If getting the ray tracer to recognize the various clipping planes is difficult, this is probably the best solution. It would be helpful, however, if Warren changed the POVray input files that are created by PyMOL a bit. One can set up all the various parts of the picture, and then selectively show each element and clip it, with the others hidden. Then output a POVray file. This should only include the visible elements (correct, Warren?). Hide this element, and show the next one, adjust the clipping plane, and output the POVray file. One can then have a master POVray file which contains as many "include" statements as are needed to bring all the various elements together in one rendered image. The difficulty in the current implementation of PyMOL is that the output for POVray contains both the scene definitions and the graphic primitives in one messy and potentially large file. If the scene definitions could be stored in one small file, and the graphic primitives in another file, this process would be much easier. One could then select one of the scene definitions files as the "master" and add "include" statements for all the graphic primitives as is needed. I suppose this process is possible with the current POVray files, just not as simple. I have examples if anybody is interested. Harry Sorry, still not done (I have made two attempts, but both failed). While OpenGL supports arbitrary clipping planes, accomplishing this correctly in the ray tracer is a much harder problem that one might think... Cheers, Warren -Original Message- From: Mankin Alexander [mailto:sh...@uic.edu] Sent: Wednesday, April 29, 2009 6:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] object-specific Z-clipping Dear all, Does anyone know whether object-selective z-clipping has been implemented in the newer Pymol version(s)? If not, has anyone found any solution around (since 2002 no new threads on the matter)? Thanks, Shura Mankin -- Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel -- Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
