[PyMOL] Plugins
Hi We are looking at possibly writing some plugins to extend the functionality of PyMOL. How would we go about this? Is there some documentation on the general process? Any help would be greatly appreciated!! -- Tjaart de Beer Bioinformatics and Computational Biology Unit University of Pretoria South Africa - The software required "Windows XP or better" ... so I installed Linux
[PyMOL] launching PyMol from a python function
I'm trying to start PyMol from another python program. After the 0_99beta17 it is possible to start it from the __main__ part of a code. But when I start PyMol from a function 'pymol.finish_launching()' goes in an endless loop. Here goes an example: --- def funct(): import __main__ __main__.pymol_argv = [ 'pymol', '-qx' ] import pymol pymol.finish_launching() print "finished" if __name__ == '__main__': funct() --- In this case PyMol window starts, but program never reaches 'print "finished"'. The same time --- if __name__ == '__main__': import __main__ __main__.pymol_argv = [ 'pymol', '-qx' ] import pymol pymol.finish_launching() print "finished" --- works fineand prints "finshed" after getting into PyMol's finish_launching() (inside __init__.py) while not hasattr(__main__,'pymol'): e.wait(0.01) Goes in an endless loop. I've tried print dir(__main__) just before this loop. When PyMol is launched not from a function, __main__ indeed have attributes '__main__' and 'pymol'. Launched from a function, there are no '__main__' or 'pymol', but 'funct'. I'll really appreciate any help or hints how make it possible to launch PyMol from a function or from a method of some class. Dmitriy
[PyMOL] rTools
Another rTools question! With the following script I get png files written for frames 1-11 and for 22-33, but none for the morphing part of the script. In fact, I cannot get any output images when running mv_morph in any context, either alone or with other commands. But the images displayed in Pymol while the mv_morph is running are exactly what I've been looking for. Is there a way to get mv_morph to write png files for every step of the morph? All I get now is a single png written at the end of the morph. I'm using rTools 0.7 with PymolX11Hybrid on OSX 10.3 Thanks again, matt mv_clear mv_set 1-11, stick_transparency, 0, 1, dTTP mv_cmd 11, disable dTTP mv_morph 12-21, pre_chem, post_chem, morph_script.pml mv_set 22-33, stick_transparency, 1, 0, post_chem_bond movie f_morph
Re: [PyMOL] question about ray after alter and rebuild
Hi Pete, Check on the sections "clipped_by" and "bounded_by" in the povray documentation. You can clip with a defined plane, and can actually do so using different planes for different objects. Alternatively you can use other objects to clip. Another possibility is to use CSG difference or intersection. Especially the latter will be painfully slow with surfaces and such, unfortunately. Come to think of it, it may be possible to directly include this in the conversion to povray. Maybe if I have a moment, I'll add it to the scripts I have and post the link... :) Cheers, Tsjerk On 10/24/05, Peter Adrian Meyer wrote: > > > > Or you can dump to povray and render at whatever resolution you want, > > but the image will not resemble exactly what is seen in the pymol viewer > > window. > > > > I've noticed problems with the clipping planes (z axis) whenever I've > tried this. Specifically, the near clipping plane is apparently not > respected in pov-ray conversion (particularly for maps/isomeshes). > I don't know if this has been fixed or not as of yet, but I wasn't able to > find a way to work around this. Your milage may vary... > > Pete > > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University > > > > --- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course > Free Certification Exam for All Training Attendees Through End of 2005 > Visit http://www.jboss.com/services/certification for more information > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
Re: [PyMOL] question about ray after alter and rebuild
> Or you can dump to povray and render at whatever resolution you want, > but the image will not resemble exactly what is seen in the pymol viewer > window. > I've noticed problems with the clipping planes (z axis) whenever I've tried this. Specifically, the near clipping plane is apparently not respected in pov-ray conversion (particularly for maps/isomeshes). I don't know if this has been fixed or not as of yet, but I wasn't able to find a way to work around this. Your milage may vary... Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] non-pdb coordinate help
Hi Kristl, The pdb-file is column formatted. You can find a specification of the file format at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html The easiest is to write a python script to do the conversion. Hope it helps, Tsjerk On 10/24/05, Kristl Adams wrote: > > I have several txt files of coordinates (mostly heme type compounds) > that I'd like to format correctly for pymol to be able to read. I've > tried several things looking at PDBs with hemes, but can't figure it out. > > Will someone with more experience please show me how this should be > formatted for pymol to read properly. > > Thanks! > > This is one of the files: (This is a heme type molecule, TPP-NO) > > FE 0.00 0.00 0.30 > N1 2.005000 0.00 0.00 > CA1 2.847000 1.093360 0.00 > CB1 4.224580 0.677440 0.00 > HB1 5.116370 1.304200 0.00 > CB2 4.224580 -0.678560 -0.00 > HB2 5.115270 -1.306870 -0.00 > CA2 2.847000 -1.094470 -0.00 > CM1 2.473030 -2.474910 -0.00 > N2 0.00 2.005000 -0.00 > CA3 -1.093360 2.847000 -0.00 > CB3 -0.677440 4.224580 -0.00 > HB3 -1.304200 5.116370 -0.00 > CB4 0.678560 4.224580 0.00 > HB4 1.306870 5.115270 0.00 > CA4 1.092590 2.847770 0.00 > CM2 2.473030 2.473800 0.00 > N3 -2.005000 0.00 0.00 > CA5 -2.847000 -1.093360 0.00 > CB5 -4.224580 -0.677440 0.00 > HB5 -5.116370 -1.304200 0.00 > CB6 -4.224580 0.678560 -0.00 > HB6 -5.115270 1.306870 -0.00 > CA6 -2.847000 1.093360 -0.00 > CM3 -2.472040 2.473520 -0.00 > N4 0.00 -2.005000 -0.00 > CA7 1.092590 -2.848880 -0.00 > CB7 0.674720 -4.225870 -0.00 > HB7 1.300210 -5.118550 -0.00 > CB8 -0.681280 -4.223950 0.00 > HB8 -1.310860 -5.113740 0.00 > CA8 -1.093360 -2.847000 0.00 > CM4 -2.472890 -2.469800 0.00 > C1 3.540060 -3.541940 0.00 > C12 4.027960 -4.029840 -1.195110 > H12 3.642590 -3.644470 -2.139080 > C13 5.003770 -5.005650 -1.195110 > H13 5.389140 -5.391020 -2.139080 > C14 5.491670 -5.493550 0.00 > H14 6.262420 -6.264300 0.00 > C15 5.003770 -5.005650 1.195120 > H15 5.389140 -5.391020 2.139080 > C16 4.027960 -4.029840 1.195120 > H16 3.642590 -3.644470 2.139080 > C2 3.540050 3.540820 0.00 > C22 4.027960 4.028730 -1.195120 > H22 3.642580 3.643350 -2.139080 > C23 5.003770 5.004540 -1.195120 > H23 5.389140 5.389910 -2.139080 > C24 5.491670 5.492440 0.00 > H24 6.262420 6.263190 0.00 > C25 5.003770 5.004540 1.195110 > H25 5.389140 5.389910 2.139080 > C26 4.027960 4.028730 1.195110 > H26 3.642590 3.643350 2.139080 > C3 -3.538280 3.541340 0.00 > C32 -4.025820 4.029600 -1.195120 > H32 -3.640730 3.643940 -2.139080 > C33 -5.000900 5.006130 -1.195120 > H33 -5.385990 5.391790 -2.139080 > C34 -5.488440 5.494400 0.00 > H34 -6.258620 6.265720 0.00 > C35 -5.000900 5.006130 1.195110 > H35 -5.385990 5.391790 2.139080 > C36 -4.025820 4.029600 1.195110 > H36 -3.640730 3.643940 2.139080 > C4 -3.542500 -3.534230 0.00 > C42 -4.031590 -4.020950 -1.195110 > H42 -3.645280 -3.636510 -2.139080 > C43 -5.009760 -4.994380 -1.195110 > H43 -5.396070 -5.378820 -2.139080 > C44 -5.498850 -5.481100 0.00 > H44 -6.271460 -6.249970 0.00 > C45 -5.009760 -4.994380 1.195120 > H45 -5.396070 -5.378820 2.139080 > C46 -4.031590 -4.020950 1.195120 > H46 -3.645280 -3.636510 2.139080 > N 0.135400 0.113610 1.981740 > O 0.660820 0.554490 2.898570 > > > --- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course > Free Certification Exam for All Training Attendees Through End of 2005 > Visit http://www.jboss.com/services/certification for more information > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
Re: [PyMOL] question about ray after alter and rebuild
Or you can dump to povray and render at whatever resolution you want, but the image will not resemble exactly what is seen in the pymol viewer window. Peter Adrian Meyer wrote: >>multiple structura alignment. I pointed out three structures for further >>processing within all 12 structures. However, when I try to ray the >>structural >>resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000, >>2000', I >>always received a low resolution (as screen resolution only) result. How >>could >>I do? Thanks a lot! > > > > Pymol can't display a ray-traced image to higher resolution than your > screen can show, but it can write it to a png file at that resolution (I'm > assuming you're talking about pixel resolution, not diffraction resolution > here). > > ray 2000,2000 ; png HighRes.png > > Pete > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University
[PyMOL] non-pdb coordinate help
I have several txt files of coordinates (mostly heme type compounds) that I'd like to format correctly for pymol to be able to read. I've tried several things looking at PDBs with hemes, but can't figure it out. Will someone with more experience please show me how this should be formatted for pymol to read properly. Thanks! This is one of the files: (This is a heme type molecule, TPP-NO) FE 0.00 0.00 0.30 N1 2.005000 0.00 0.00 CA1 2.847000 1.093360 0.00 CB1 4.224580 0.677440 0.00 HB1 5.116370 1.304200 0.00 CB2 4.224580 -0.678560 -0.00 HB2 5.115270 -1.306870 -0.00 CA2 2.847000 -1.094470 -0.00 CM1 2.473030 -2.474910 -0.00 N2 0.00 2.005000 -0.00 CA3 -1.093360 2.847000 -0.00 CB3 -0.677440 4.224580 -0.00 HB3 -1.304200 5.116370 -0.00 CB4 0.678560 4.224580 0.00 HB4 1.306870 5.115270 0.00 CA4 1.092590 2.847770 0.00 CM2 2.473030 2.473800 0.00 N3 -2.005000 0.00 0.00 CA5 -2.847000 -1.093360 0.00 CB5 -4.224580 -0.677440 0.00 HB5 -5.116370 -1.304200 0.00 CB6 -4.224580 0.678560 -0.00 HB6 -5.115270 1.306870 -0.00 CA6 -2.847000 1.093360 -0.00 CM3 -2.472040 2.473520 -0.00 N4 0.00 -2.005000 -0.00 CA7 1.092590 -2.848880 -0.00 CB7 0.674720 -4.225870 -0.00 HB7 1.300210 -5.118550 -0.00 CB8 -0.681280 -4.223950 0.00 HB8 -1.310860 -5.113740 0.00 CA8 -1.093360 -2.847000 0.00 CM4 -2.472890 -2.469800 0.00 C1 3.540060 -3.541940 0.00 C12 4.027960 -4.029840 -1.195110 H12 3.642590 -3.644470 -2.139080 C13 5.003770 -5.005650 -1.195110 H13 5.389140 -5.391020 -2.139080 C14 5.491670 -5.493550 0.00 H14 6.262420 -6.264300 0.00 C15 5.003770 -5.005650 1.195120 H15 5.389140 -5.391020 2.139080 C16 4.027960 -4.029840 1.195120 H16 3.642590 -3.644470 2.139080 C2 3.540050 3.540820 0.00 C22 4.027960 4.028730 -1.195120 H22 3.642580 3.643350 -2.139080 C23 5.003770 5.004540 -1.195120 H23 5.389140 5.389910 -2.139080 C24 5.491670 5.492440 0.00 H24 6.262420 6.263190 0.00 C25 5.003770 5.004540 1.195110 H25 5.389140 5.389910 2.139080 C26 4.027960 4.028730 1.195110 H26 3.642590 3.643350 2.139080 C3 -3.538280 3.541340 0.00 C32 -4.025820 4.029600 -1.195120 H32 -3.640730 3.643940 -2.139080 C33 -5.000900 5.006130 -1.195120 H33 -5.385990 5.391790 -2.139080 C34 -5.488440 5.494400 0.00 H34 -6.258620 6.265720 0.00 C35 -5.000900 5.006130 1.195110 H35 -5.385990 5.391790 2.139080 C36 -4.025820 4.029600 1.195110 H36 -3.640730 3.643940 2.139080 C4 -3.542500 -3.534230 0.00 C42 -4.031590 -4.020950 -1.195110 H42 -3.645280 -3.636510 -2.139080 C43 -5.009760 -4.994380 -1.195110 H43 -5.396070 -5.378820 -2.139080 C44 -5.498850 -5.481100 0.00 H44 -6.271460 -6.249970 0.00 C45 -5.009760 -4.994380 1.195120 H45 -5.396070 -5.378820 2.139080 C46 -4.031590 -4.020950 1.195120 H46 -3.645280 -3.636510 2.139080 N 0.135400 0.113610 1.981740 O 0.660820 0.554490 2.898570
Re: [PyMOL] Adjust radius of sphere
Hi Anbang Li, If you want to show the spheres in a relative size, you can use set sphere_scale, 0.5 to scale down the size by half for example. To do this for a specific object, use set sphere_scale, 0.5, object Otherwise, if you want to change the actual radius, you can use alter selection, vdw=newradius Possibly you have to use rebuild to update the scene afterwards. Cheers, Tsjerk On 10/24/05, Li Anbang wrote: > > Hi all, > > I have a question about radius of sphere: I select a atom, show its > sphere, then I want to increase the radius of sphere. How to do this? > > Thanks for answers. > Anbang Li > > > --- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course > Free Certification Exam for All Training Attendees Through End of 2005 > Visit http://www.jboss.com/services/certification for more information > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
Re: [PyMOL] question about ray after alter and rebuild
> multiple structura alignment. I pointed out three structures for further > processing within all 12 structures. However, when I try to ray the > structural > resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000, > 2000', I > always received a low resolution (as screen resolution only) result. How > could > I do? Thanks a lot! Pymol can't display a ray-traced image to higher resolution than your screen can show, but it can write it to a png file at that resolution (I'm assuming you're talking about pixel resolution, not diffraction resolution here). ray 2000,2000 ; png HighRes.png Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] Adjust radius of sphere
Hi all, I have a question about radius of sphere: I select a atom, show its sphere, then I want to increase the radius of sphere. How to do this? Thanks for answers. Anbang Li
