Re: [PyMOL] how to get RMSD from align command
Tom, Because the number of atoms in the alignment can vary with each pairwise structure comparison, the RMS number returned by align cannot be considered valid criterion except perhaps if presented along with the number of atoms in each comparison. E.g.: RMS over X atoms 0.5 1451 0.3 1273 0.4 1343 But remember, each final RMS value will involve a different set of atoms...and that's the root of the problem...there's no common reference point. Therefore, I must recommand against using 'align' for this purpose -- it's just not the right tool for the job. Cheers, Warren -Original Message- From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] Sent: Thursday, October 29, 2009 4:56 PM To: Warren DeLano Cc: Thomas Evangelidis; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] how to get RMSD from align command Warren, before I write something incorrect into Methods section, do you think the overall RMSD returned by align command is a valid criterion to select which structure of the family is most similar? Tom Tom, Apologies for the confusion, but there really isn't any way to measure overall structural similarity in PyMOL other than pair_fit, but you have to do the work of explicitly stating which pairs are to be aligned. The pair_fit selections don't have to be identical, but they do have to correspond in a pairwise fashion. In other words, you can compare any number of C-alpha positions so long as the same number of atomic positions are specified in each structure. Cheers, Warren -Original Message- From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] Sent: Thu 10/29/2009 5:24 AM To: Warren DeLano Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] how to get RMSD from align command Hi Warren, Now I am more confused. I used align command to measure the overall RMSD between homologous structures. Apparently align is not appropriate if not sufficient sequence similarity is present. I later came across CEalign plugin, which does structure-based superimposition. This command also returns an RMSD value, which happens to be higher for the set of homologous structures I analysed. Based on this I concluded that align command is more appropriate to measure measure structural similarity, but I'm not sure now. My objective is to select between a small set of homologous structures (co-crystallized with ligands), the one with the highest structural similarity and use it to place a dummy ligand into one where it's missing. I.e. 1ebh lacks a ligand, so I compared it with 1ebg, 1els, 1one, 2one, 5enl, 6enl, 7enl which have co-crystallized ligands. According to both align and cealign, 5ENL is the most similar with overall RMSD 0.246 and 0.420907 respectively. The question is which command produces the best superimposition provided that these proteins belong to the enolase family and thus have high sequence and structural similarity? Based on the RMSD values, align does, but as you said this value pertains to only a subset of atoms after refinement. Apparently pair_fit command cannot be used for my purpose as it requires identical selections. Tom Tom, The complication with cmd.align() is that it is doing a whole lot more than a simple alignment. The first number is in fact the RMS, but it covers only the subset of the input atoms remaining after refinement is completed. The count of aligned atoms is the second field. If you're looking for exact RMS fit values over a well-defined set of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example: load $TUT/1hpv.pdb create loopA, A/46-55/ create loopB, B/46-55/ show sticks, loop* print cmd.pair_fit(loopACA, loopBCA) Cheers, Warren -Original Message- From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] Sent: Wed 10/28/2009 8:09 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] how to get RMSD from align command Simple question, it must have been answered before but couldn't find it so far: how can I get the RMSD value from the align command in a python script? cmd.align() returnes a tuple of 8 numbers and none of them is the actual RMSD value I get when I align these 2 structures manually. thanks,Tom --- --- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http
Re: [PyMOL] how to get RMSD from align command
Tom, Apologies for the confusion, but there really isn't any way to measure overall structural similarity in PyMOL other than pair_fit, but you have to do the work of explicitly stating which pairs are to be aligned. The pair_fit selections don't have to be identical, but they do have to correspond in a pairwise fashion. In other words, you can compare any number of C-alpha positions so long as the same number of atomic positions are specified in each structure. Cheers, Warren -Original Message- From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] Sent: Thu 10/29/2009 5:24 AM To: Warren DeLano Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] how to get RMSD from align command Hi Warren, Now I am more confused. I used align command to measure the overall RMSD between homologous structures. Apparently align is not appropriate if not sufficient sequence similarity is present. I later came across CEalign plugin, which does structure-based superimposition. This command also returns an RMSD value, which happens to be higher for the set of homologous structures I analysed. Based on this I concluded that align command is more appropriate to measure measure structural similarity, but I'm not sure now. My objective is to select between a small set of homologous structures (co-crystallized with ligands), the one with the highest structural similarity and use it to place a dummy ligand into one where it's missing. I.e. 1ebh lacks a ligand, so I compared it with 1ebg, 1els, 1one, 2one, 5enl, 6enl, 7enl which have co-crystallized ligands. According to both align and cealign, 5ENL is the most similar with overall RMSD 0.246 and 0.420907 respectively. The question is which command produces the best superimposition provided that these proteins belong to the enolase family and thus have high sequence and structural similarity? Based on the RMSD values, align does, but as you said this value pertains to only a subset of atoms after refinement. Apparently pair_fit command cannot be used for my purpose as it requires identical selections. Tom Tom, The complication with cmd.align() is that it is doing a whole lot more than a simple alignment. The first number is in fact the RMS, but it covers only the subset of the input atoms remaining after refinement is completed. The count of aligned atoms is the second field. If you're looking for exact RMS fit values over a well-defined set of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example: load $TUT/1hpv.pdb create loopA, A/46-55/ create loopB, B/46-55/ show sticks, loop* print cmd.pair_fit(loopACA, loopBCA) Cheers, Warren -Original Message- From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] Sent: Wed 10/28/2009 8:09 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] how to get RMSD from align command Simple question, it must have been answered before but couldn't find it so far: how can I get the RMSD value from the align command in a python script? cmd.align() returnes a tuple of 8 numbers and none of them is the actual RMSD value I get when I align these 2 structures manually. thanks,Tom -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 - End message from war...@delsci.com - -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu
[PyMOL] Remember, PyMOL is for visualization, not analysis.
Dear PyMOL-Users: Today's questions regarding alignment RMS values suggest to me that I should re-emphasize what PyMOL is and is not good for: Please everyone keep in mind that PyMOL is intended to be just a molecular graphics program, to be used for displaying, comparing, and manipulating molecular structure in various visual and interactive ways. PyMOL is a figure maker, a movie maker, a presentation tool -- a molecular communications platform, if you will. PyMOL is not intended to be, nor should it be used as, a molecular analysis tool. It wasn't built with that goal in mind, and most of the algorithms inside the program have not been rigorously validated. As a general rule, if the numbers matter, then you should be using other more rigorous software for those tasks, and then loading only the final output into PyMOL (for rendering, etc.). Thank you all for keeping this in mind as you continue to apply PyMOL in your work. Cheers, Warren -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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] Replace Coordinates in State
Sean, Unfortunately, there isn't any way at present to directly expose PyMOL's internal C coordinate array to Python in an accessible form. Yes, iterate_state and alter_state are highly inefficient - it would make more sense to provide a means of exporting and re-importing coordinate sets via either native Python lists or, even better, NumPy arrays. In what form do you have the current coordinate data? Cheers, Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Friday, October 23, 2009 4:54 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Replace Coordinates in State Hi All, I was wondering if there was a faster way to replace all coordinates. I've used commands such as iterate_state and alter_state before but they are far too slow since they have to iterate over each atom. Instead, I want to replace one set of coordinates that correspond to a specific state with a different set. Here's what I have to work with: I have a list that contains x, y, z coordinates. Of course, this list can be manipulated and/or separated if necessary. I'm assuming that the coordinates for a specific state are stored somewhere in memory and I would basically like to replace one set of coordinates with the other. I would think that something like pointers or references would work a lot faster than having to copy the coordinates over (which is typically slow and is likely what alter_state is doing?). In addition, I am dealing with 100+ states using alter_state for each state would be far too slow. Any suggestions would be greatly appreciated. Thanks in advance! Sean Save up to 84% on Windows 7 until Jan 3-eligible CDN College or University students only. Hurry-buy it now for $39.99! http://go.microsoft.com/?linkid=9691631 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ 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] number of h-bonds
Hello Michael, Unfortunately, there is no programmatic way to get this information out of PyMOL -- my apologies! Cheers, Warren -Original Message- From: Michael Zimmermann [mailto:micha...@iastate.edu] Sent: Mon 10/26/2009 9:04 PM To: pymol-users Subject: [PyMOL] number of h-bonds Dear PyMOL users, I was using Action - find - polar interactions within selection to get an idea about the hydrogen bonds and other polar interactions in some molecules. I would like to compare different conformations of a certain molecule and one metric could be the number of pair returned by one of these distance evaluations. Could someone help me figure out how to get routines like this to return the number of pairs that they define? Alternatively, for the object that is returned, is there a way to loop through the line objects or labels and count them? Thank you. -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ 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] Pymol Align Command and RMSD Calculation ?
1. What type of RMSD is calculated with align comman i.e All Atoms or only Backbone? It depends on the input selections. If you don't restrict it to backbone atoms, PyMOL will perform the fit for all matched atoms. Also, it is important to understand that align is a combined sequence and 3D refined structure alignment which, by default, iteratively discards outliers in order to achieve a well-matched core structure. super is similar except that it doesn't use sequence. 2. If I have few models/PDB stuructures of the same protein how I can clauclate the total atoms and backbone only RMSD between these. Actually I am confused with usuage of these commands i.e align , super, rms, rms_cur etc. If you're trying to calculate RMS between specific pairs of atoms : If the proteins have matched identifiers (identical segment, chain, and residue identifier), then the command you want is fit: # all atom fit obj1, obj2 # C-calpha only fit obj1CA, obj2CA If the protein do not have matched identifiers, then you must manually select exactly N atom pairs in each structure, and then use pair_fit: # C-alpha fit for residues 10 through 80 and 100 through 120 pair_fit obj1///10-80+100-120/CA, obj2///10-80+100-120/CA Cheers, Warren From: Bio Brain [mailto:biobr...@gmail.com] Sent: Sat 10/24/2009 1:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol Align Command and RMSD Calculation ? Dear Pymol Users, I am looking for some very basic information about the PyMol commands. 1. What type of RMSD is calculated with align comman i.e All Atoms or only Backbone? 2. If I have few models/PDB stuructures of the same protein how I can clauclate the total atoms and backbone only RMSD between these. Actually I am confused with usuage of these commands i.e align , super, rms, rms_cur etc. Regards -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ 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] not getting a simple translation
Hi David, You have a rotate command in that script. Did you mean to 'turn' the camera rather than 'rotate' the atomic coordinates? Cheers, Warren -Original Message- From: David Garboczi [mailto:dgarbo...@niaid.nih.gov] Sent: Thursday, October 22, 2009 7:00 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] not getting a simple translation I have a 5 similar domains (struct.pdb) aligned on another one (rcsb.pdb). I made a copy of one of them and translated it 37 angstroms to the right. translate [37, 0, 0 ]. But I did not get a simple translation. The two molecules end up having a rotation between them. Here's the script. I need an origin command or other...? thanks, Dave #macpymol-1_1r1.tgz reinitialize bg_color white set antialias , 1 set ray_trace_fog=0 set depth_cue=0 set direct, 0.7 set ribbon_smooth, 1 set ribbon_width, 3 set_view (\ -0.342648655,0.901220083, -0.265300900,\ 0.939403236,0.325558662, -0.107372068,\ -0.010394786, -0.286019355, -0.958166420,\ 0.0,0.0, -128.319412231,\ 22.162364960, 43.079395294, 12.406776428,\ 101.167999268, 155.470825195,0.0 ) load rcsb.pdb, rcsb2 load rcsb.pdb, a33alone #1kcg:A load struct(2).pdb, 22 #1e8i:A load struct(3).pdb, 33 #1ypo:A load struct(4).pdb, 44 #1B6E_dimer.pdb:A load struct(5).pdb, 55 #1qo3:C load struct(6).pdb, 66 hide lines, /rcsb2//* hide nonbonded, /rcsb2//* hide lines, /a33alone//* hide nonbonded, /a33alone//* hide lines, /22//* hide nonbonded, /22//* hide lines, /33//* hide nonbonded, /33//* hide lines, /44//* hide nonbonded, /44//* hide lines, /55//* hide nonbonded, /55//* hide lines, /66//* hide nonbonded, /66//* color red, /a33alone//* show ribbon, /a33alone//* and (name ca or name c or name n) color red, /rcsb2//* show ribbon, /rcsb2//* and (name ca or name c or name n) color yelloworange, /22//* color blue, /22//A/98-134/* color blue, /22//A/190-215/* show ribbon, /22//* and (name ca or name c or name n) color yelloworange, /33//* color blue, /33//A/83-121/* color blue, /33//A/174-199/* show ribbon, /33//* and (name ca or name c or name n) color yelloworange, /44//* color blue, /44//A/142-180/* color blue, /44//A/244-269/* show ribbon, /44//* and (name ca or name c or name n) color yelloworange, /55//* color blue, /55//A/60-97/* color blue, /55//A/153-179/* show ribbon, /55//* and (name ca or name c or name n) color yelloworange, /66//* color blue, /66//C/144-175/* color blue, /66//C/233-258/* show ribbon, /66//* and (name ca or name c or name n) hide ribbon, /66//C/140-143/* rotate y, 30 set_view (\ -0.287066191,0.957891881,0.004756007,\ 0.607159078,0.178112596,0.774357498,\ 0.740909398,0.225178465, -0.632728696,\ 0.0,0.0, -191.885284424,\ 24.745697021, 46.720252991, 14.490940094,\ 151.283813477, 232.486755371,0.0 ) translate [37, 0, 0 ], a33alone zoom complete=1 #ray 4800,4800 #png /Users/dgarboczi/Documents/A_on_A/A_on_A_2_newview_4.png, dpi=600 -- -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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] real time first person camera view / control
Nick, How would this be different from the existing Scene interpolation capability? You can use the Scene menu to Append a series of scenes of the molecule (views+representations) and then use Scene - Next, PAGE-DN or the scene command to interpolate through them. Cheers, Warren From: Nick Hunter [mailto:nickhunt...@googlemail.com] Sent: Thursday, October 22, 2009 6:24 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] real time first person camera view / control hello - i would like to create a first person view so that it is as if you are walking around the scene. would this be possible through pymol's python interface while maintaining adequate performance for real time interaction? if not, would it be possible/difficult to alter the source code in such a way that the camera view control may be set up to mimic a first person view of the scene? thanks, nick -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ 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] Saving high resolution images
Hi Tom, Actually this is how the draw command works in using the screen-based OpenGL renderer to create images of arbitrary size. However, the ray-tracer isn't currently set up to operate that way. Ray might work with an orthoscopic projection, but with perspective enabled, each frame would have a distinct vanishing point (if that's the correct term). Cheers, Warren From: Thomas Stout [mailto:tst...@exelixis.com] Sent: Thu 10/22/2009 12:36 PM To: Tsjerk Wassenaar Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Saving high resolution images But isn't it true that only the objects that are visible in the viewport are what are written to the rendered image file? I was proposing rendering a poster-sized image in tiles and stitching them back together post facto to create a very large, high resolution image. something like: --- | | | | | | | render 1 | render 2 | | | | | | | |-- | | | | | | | render 3 | render 4 | | | | | | | --- I feel like I'm missing something important here! -Tom -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Thursday, October 22, 2009 11:45 AM To: Thomas Stout Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Saving high resolution images Hi Thomas, The viewport is not important for rendering. You can render at whatever resolution/dimensions you want with whatever viewport. You can even make a panorama using a wide angle lens if you want to have something for on your wall ;) Cheers, Tsjerk On Wed, Oct 21, 2009 at 11:43 PM, Thomas Stout tst...@exelixis.com wrote: Here's a crazy idea: if someone out there were clever at both python and manipulating orientation matrices, I would bet that a scene could be quartered or cut into eighths and translated such that each portion filled the viewport for rendering; then the individual images could be spliced back together in one's favorite image handling program a la panoramas in photography Is this way too complex to be bothered with? I suspect parallax may be a problem... -Tom -Original Message- From: Eva Vanamee [mailto:eva.vana...@mssm.edu] Sent: Monday, October 19, 2009 1:51 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Saving high resolution images Hi, I'd like to save an image in high resolution for a poster. The requested size is 20 by 30. I calculated that it would correspond to a 6000 x 9000 pixel image. How can I create such a large ray traced image without crashing the computer? Many thanks in advance for the help. Best, - Eva -- -- -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems. -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the
Re: [PyMOL] Secondary Structure Matching
Fred, You might try super instead of align (same syntax). Failing that, you can use pair_fit with explicit selections -- just make sure the number of atoms is the same in each of the selections. Cheers, Warren -Original Message- From: Kerff Frédéric [mailto:fke...@ulg.ac.be] Sent: Wednesday, October 21, 2009 5:51 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Secondary Structure Matching Hello, Is there a way to perform secondary structure matching with Pymol. I already tried the align function with different selections without any success but the 2 proteins obviously share the same fold with low sequence identity. I know it can be done in other software like Coot but I'd like to avoid having to switch from one program to another all the time. Thank you. Fred -- Frédéric Kerff Chargé de recherche F.R.S.-FNRS Cristallographie des protéines Centre d'Ingénierie des Protéines Université de Liège - Bat B5a B4000 Liège (Sart-Tilman) Tel.: +32 (0)4 3663620 Fax: +32 (0)4 3663772 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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] Saving high resolution images
Eva, You may be past the limit of what PyMOL can handle. Regardless, the 64-bit Linux builds are the best at handling large-memory tasks. Practice with something really simple: fragment arg as spheres ray 6000,9000 Also, two more things I'd suggest for such a large image (in order to cut down on RAM usage): set antialias,0 set hash_max, 100 ray 6000,9000 Another thing you can do is render 3000,4500 and use Photoshop to subsample. Cheers, Warren -Original Message- From: Eva Vanamee [mailto:eva.vana...@mssm.edu] Sent: Monday, October 19, 2009 2:12 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Saving high resolution images Hi, I'd like to save an image in high resolution for a poster. The requested size is 20 by 30. I calculated that it would correspond to a 6000 x 9000 pixel image. How can I create such a large ray traced image without crashing the computer? Many thanks in advance for the help. Best, - Eva -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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] selecting multiple, non-adjacent chains
Sean, There is also a more concise option: select allothers, chain 0:4+C:J+L:Z Or even more concise, using selection macro: chain/residue/atom select allothers, 0:4+C:J+L:Z// Cheers, Warren -Original Message- From: Marius Retegan [mailto:marius.s.rete...@gmail.com] Sent: Thursday, October 15, 2009 7:13 AM To: Sean Moore Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] selecting multiple, non-adjacent chains Try this one select allothers, chain 0:4 or chain C:J or chain L:Z Marius On Thu, Oct 15, 2009 at 3:34 PM, Sean Moore semo...@mail.ucf.edu wrote: Hello, I am trying to find an easier way to select multiple chains at once in a large file with many chains (PDB 2i2t). The chain assignments exceed z and start again at 0 at the beginning of the chain list. In an effort to select chain 0-4, skip chain A+B, select chain C-J, skip chain K, and select the remaining L-Z, I have tried (among other things): select allothers, chain 0-4 and C-J and L-Z (the dashes don't seem to work for select) select allothers, chain 0:4 and C:J and L:Z select allothers, chain 0:4 and chain C:J and chain L:Z select allothers, (chain 0:4) and (chain C:J) and (chain L:Z) selecting chain 0+4 works, and selecting chain 0:4 works. As it stands I have to click all of the chains then rename the selection which leads to mistakes. Any help is appreciated. -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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] Change location of measurement label
Switch the mouse into editing mode, then ctrl-left-click-and-drag on the label to reposition. Cheers, Warren -- Warren L. DeLano, Ph.D. war...@delsci.com (Sent from an iPhone -- please forgive brevity and/or typos!) On Oct 14, 2009, at 8:03 AM, Per Larsson per.lars...@sbc.su.se wrote: Hi! I need to make some pictures of very simple di-peptide systems, and need to include values (from wizard-measurement-dihedrals) of certain dihedral angles. However, the two labels end up very close, with the values almost on top of each other making them un-readable. Is there a way to change the location of the measurement labels? Thanks! /Per --- --- --- - Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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] color functionality for mac versions
Mark ( indeed all Mac users) MacPyMOL can be launched in two flavors, based on the name of the executable: If the executabled is named MacPyMOL, PyMOL launches in the mode you're familiar with: a single-window Cocoa-based interface. If the executable is renamed PyMOLX11Hybrid, then PyMOL launches using the Tcl/Tk/X11-based, two-window interface you're familiar with from Windows and Linux. That's how you can get at the color slider you seek. Cheers, Warren -Original Message- From: mnc2...@columbia.edu [mailto:mnc2...@columbia.edu] Sent: Thursday, October 08, 2009 10:50 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] color functionality for mac versions Hi I was talking to a fellow student about coloring different molecules in an image for publication. And one reviewer suggested the 3 colors he was using were different of luminocity. He then showed me where to adjust this in the PC version. Setting Colors... , and adjust or create new colors. I'm a mac user, and both macpymol and the hybrid version have only red, blue and green sliders in the modify colors menu. No Lum. slider or h/l/s boxes. I am missing something? I really like this functionality on the pc version. Thanks Mark -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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] rmsd for multiple snaphosts
Dear all, i have multiple conformations files (multi pdb) and would like to compute for each one, the rmsd for each snapshot against the first snapshot. Is it possible with pymol to do such a task ? thank you in advance for the gain of time ... :-) nicolas floquet Yes, using a short Python loop: # .pml example PyMOL script # load structure into input object fetch 1nmr, input, async=0 # choose the reference state create ref, input, 1, 1 # now iterate using Python python for i in range(cmd.count_states(input)): cmd.create(tmp, input, i+1, 1) print 1, i+1, cmd.fit(tmp, ref) cmd.delete(tmp) python end # end example Cheers, Warren -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] Sessions and Scope
Tsjerk, Great question with a crummy answer: you can't! But this seems like a really good idea, at least for primitives stored in ordinary built-in Python containers. Saving class instances would be problematic, since session files wouldn't necessarily be restorable in the absence of accompanying class definitions [we do rely upon Python pickling machinery, and are thus subject to its limitations]. Cheers, Warren -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Friday, October 02, 2009 6:04 AM To: pymol-users Subject: [PyMOL] Sessions and Scope Hi, At present I'm setting some variables in the globals() dictionary/global scope, but when I save the session, these variables are lost. What would be the best way to preserve them? (This question may also be interpreted as: what does Pymol write to a session file?). Cheers, Tsjerk -- 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] DepthQ configuration in a classroom setting
Roger, That's a bit odd: usually it either works or it doesn't. Working for 20 seconds at a time may indicate defective hardware (projector, emitter, graphics card, connector, dead battery, etc.). But as a first test, pease try using some other stereo-3D-capable software (e.g. VMD or Chimera) in order to make certain that the problem is not due to PyMOL itself. Cheers, Warren From: Roger Rowlett [mailto:rrowl...@colgate.edu] Sent: Tuesday, September 29, 2009 9:58 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] DepthQ configuration in a classroom setting Has anyone on the board configured a DepthQ projector for classroom use, i.e. using a ceiling-mounted projector. Our IT department has recently installed a DepthQ projector in a classroom-type setting, and it displays stereo Pymol images for about 20 seconds, then loses sync. My configuration is the following: Intel WinXP PC with Quadro 3700 running NVidia driver 191.00 Stereo ON enabled in the Global settings of the Nvidia Control panel DepthQ installed as only graphical display device (currently) Screen resolution set to the native resolution of the DepthQ projector I'm running a recent version (1.2) of Pymol I assume that to get a second monitor display of the DepthQ projector I should attach a VGA cable to the video out port of the DepthQ and run that to an appropriate LCD monitor. Am I missing anything? I'm wondering if the video cabling is too long or inappropriate, causing the sync dropouts, or if I have missed something really elementary in the Nvidia configuration. At this point, I'm considering breaking down the classroom installation and testing the computer and projector on the bench. Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ 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] Iterate Script Over States
Sean, I'm not sure what you have in mind other than something like (python code): for state in cmd.count_states(): cmd.iterate_state(state, selection, expression) where expression is accumulating coordinates from multiple states Cheers, Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Monday, September 28, 2009 7:14 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Iterate Script Over States Hi PyMOL Users, I was wondering if there was a smart way of having a script iterate over all (or some) of the states. I know that there are the usual iterate and iterate_state commands available but it appears that it makes for clumsier code. More specifically, I'm looking to use the pucker.py script which calculates sugar dihedral angles (found under PUCKER at the PyMOL-Wiki) and have it spit values back for all states of an MD simulation rather than just only the first state. Basically, I would like for it to behave like the distance/dihedral measurement functions available in the PyMOL wizard such that the pucker information is calculated, displayed on the screen, and changes as I run through each frame. Thanks in advance! Sean Attention all humans. We are your photos. Free us. -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] Iterate Script Over States
Sean, Yes, that is an alternate route. cmd.get_model is likely slower than cmd.iterate_state, but should work regardless. Cheers Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Monday, September 28, 2009 11:58 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Iterate Script Over States I think I figured it out (though, it wasn't documented). What I needed was to use: cmd.get_model(selection, STATE) I think that's the correct usage? What I needed was to loop through a selection and then to calculate the sugar pucker information. However, not all atoms from the selection are required for the calculation so some pre-parsing of the residue is needed. It appears that I can specify the state to obtain atom objects from via the get_model command. I hope that is right? Sean Create a cool, new character for your Windows Live(tm) Messenger. Check it out http://go.microsoft.com/?linkid=9656621 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ 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] Loading PDB Files does not work with Linux
Joachim, PyMOL relies entirely upon Python's built-in proxy support (via urllib), so if you can get a Python script configured to work properly through your proxy, then PyMOL should work as well. http://www.python.org/doc/2.5.2/lib/module-urllib.html Cheers, Warren From: greipel.joac...@mh-hannover.de [mailto:greipel.joac...@mh-hannover.de] Sent: Thursday, September 24, 2009 5:51 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Loading PDB Files does not work with Linux Hi all, I can't get the functions to load pdb-data from the internet to work under Linux. Neither fetch nor load http://...; nor the plugin remote_pdb_load.py will work (connection error - please check your internet access). Under windows at least the load... method and the plugin are operable, the fetch method does not work either. The familiar plugin ProxyConfig.py also is of no use. The Pymol versions are 1.0 and 1.2r1. We have to use a http-proxy, but the proxy-url and -port are present in the environment variable http_proxy. I would really like to use Linux, so, do you have any hints? How should I setup pymol as to use the proxy? Regards, Joachim -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ 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] Pymol segmentation fault
Ian, Based on that traceback, it looks like you have two conflicting versions of Tcl (8.4 as well as 8.5) linked against and running in the same process...that could be the source of the crash. Cheers, Warren From: Ian Berke [mailto:ian.be...@yale.edu] Sent: Thursday, September 24, 2009 11:26 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol segmentation fault Hi, I'm having an issue trying to run various plugins in pymol (apbs and autodock). Whenever I select a button that should bring up a file browser to choose a file (e.g. Choose Externally generated pqr in apbs) Pymol exits with: Segmentation fault (core dumped). Same thing happens when I go to HelpAbout. I can open and save files normally, and just about everything else works. I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin window to open, as well as the 1.2 trunk from svn (downloaded and compiled last week) which just crashes when I try to open the apbs window (I can install autodock.py and the window opens, but it crashes when I try to choose the location of files). I'm guessing this is something to do with the gui and tcl/tk, but don't have any idea how to troubleshoot (see the catchsegv output below). I'm running Ubuntu 9.10 on x86_64 and have a GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36. Does anyone have any thoughts? Here is the backtrace portion from catchsegv: Backtrace: /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0] /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839] /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f] /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b] /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b] /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9] /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f] /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859] /usr/lib/libtcl8.5.so.0[0x7f639777dee6] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f6397710a5f] /usr/lib/libtcl8.5.so.0[0x7f63977926d1] /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209] /usr/lib/libtcl8.5.so.0[0x7f6397793192] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413] /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32] /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python[0x52bdf0] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python[0x4254ff] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623] /usr/bin/python[0x49c06f] /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python[0x52bdf0] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python[0x4254ff] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623] /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376] /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0[0x7f63977527b9] /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706] /usr/lib/libtk8.5.so.0[0x7f6397a556f6] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413] /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870] /usr/lib/libtcl8.5.so.0[0x7f639779668f] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
Re: [PyMOL] mutation
Chandan, Apologies, but PyMOL can only mutate the standard 20 amino acids. Note that you have asked that second question before: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07211.h tml Again, there is no special theory behind PyMOL's mutagenesis wizard: the intent behind the implementation is to simply provide geometric substitution as per the Dunbrack rotomer library. No optimization is performed. Please follow the link below for a list of related references covering the Dunbrack library and sidechain rotamer theory: http://dunbrack.fccc.edu/bbdep/bbdepdownload.php Cheers, Warren From: Chandan Choudhury [mailto:iitd...@gmail.com] Sent: Tuesday, September 22, 2009 9:28 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] mutation Hello all!! I am required to mutate one of the atom of a protein (pdb file) with some groups of atoms. Pymol features us to mutate a residu with another amino acid, but I cannot mutate an atom with some other group that are not amino acids. So, how can I do it. Please help. Also I want to know the theory behind the mutation of residue done by pymol. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ 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] dihedral angle
Vivek, If there are multiple attached atoms, then there may be multiple dihedrals present. There is a visual indicator which shows what angle is being measured -- do those indicator match the displayed angle? Cheers, Warren -Original Message- From: Vivek Ranjan [mailto:vran...@gmail.com] Sent: Tuesday, September 22, 2009 1:51 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] dihedral angle Hello, When I cntrl+right-click on a bond, it is supposed to give the dihedral angle. However, it gives something else. E.g. the angle in question has actual dihedral angle of 180 degrees. However, it shows -56.9 degrees. Please let me know how this works ? -- Thank you and Regards, Vivek Ranjan -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] dash_radius
Craig, In the OpenGL viewer, dashes are always drawn using line primitives, so dash_radius has no effect until you issue the ray command. Note that dash_width is generally preferable to dash_radius since it controls both the OpenGL and ray-traced renditions (so long as dash_radius is zero). Cheers, Warren -Original Message- From: Craig Smith [mailto:boiler...@mac.com] Sent: Tuesday, September 22, 2009 1:59 PM To: pymol-users@lists.sourceforge.net Cc: csmi...@lindenwood.edu Subject: [PyMOL] dash_radius Hello, I trying to make thicker and longer dashes for indicating distances for a figure I'm making. I can make the the dashes longer with dash_length. But, the dashes look very flat. I tried making the dashes look rounder using dash_radius. When I change the value I don't see a change in the dashes or anything else. So, what does dash_radius do? How do I make the dashes look rounder/ Craig -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] Bond command not functioning in script
Stuart, For what's it's worth, I'm not able to reproduce the problem: Aside from automatic suppression of output when using the Python API, I'm getting the exact same behavior with # test1.pml cmd.pseudoatom(temp,pos=[0,0,0],name=A) cmd.pseudoatom(temp,pos=[0,0,5],name=B) cmd.bond(tempA,tempB) # test2.pml pseudoatom temp,pos=[0,0,0],name=A pseudoatom temp,pos=[0,0,5],name=B bond tempA,tempB # and test3.pml python cmd.pseudoatom(temp,pos=[0,0,0],name=A) cmd.pseudoatom(temp,pos=[0,0,5],name=B) cmd.bond(tempA,tempB) python end Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, September 21, 2009 3:53 PM To: pymol-users Subject: [PyMOL] Bond command not functioning in script Hello all, Warren, I have a script which creates two pseudoatoms and a bond object between them, but the bond step consistently fails. However, the two pseudoatoms can be bound in the console after the script halts with the exact same command which fails in the script: cmd.bond(temp0A0,temp0B0) Alternatively, cmd.do(bond temp0A0, temp0B0) fails just the same. The following works perfectly: PyMOLpython 1:cmd.pseudoatom(temp,pos[0,0,0],name=A) 2:cmd.pseudoatom(temp,pos[0,0,5],name=B) 3:cmd.bond(tempA,tempB) PyMOLpython end So can anyone tell me why the exact same thing in a script halts after 2? Thanks, Stuart Ballard Dept. of Biochemistry University of Wisconsin-Madison -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] Grid View of a Group
Yes, but it may not be the answer you want: avoid putting those objects into groups. At present, groups and grids are interconnected in a hard-coded manner. Cheers, Warren -Original Message- From: T. Andrew Binkowski [mailto:abinkow...@anl.gov] Sent: Thursday, September 17, 2009 9:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Grid View of a Group Hi, I noticed that in the Grid view that a group of objects is in each view. For example: Group A has protein1, protein2 and protein 3. Group B has protein 4 and protein 5. In the grid view there are two views:Group A and GroupB. Is it possible to have the grid view have 5 views, one of each molecule? Thanks, Andrew -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] Displaying electron density from maps output by Coot.
To Everyone: When posting such questions, please always indicate what specific vesion of PyMOL you are using, since the program continues to evolve with every release (to reflect numerous end-user suggestions, as enabled by contributions from our sponsors.) To Andy: PyMOL version 1.2r1 should symmetry-expand the map assuming that density values have been provided somewhere within the ASU. PyMOL cannot yet render a map straight from a reflection file. Cheers, Warren -Original Message- From: Andy Torelli [mailto:at...@cornell.edu] Sent: Thursday, September 17, 2009 11:54 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Displaying electron density from maps output by Coot. Hi everyone, I have a simple problem that has come up before (4/2/2009 post), but I haven't found a solution yet. Maps written out from Coot and display in Pymol seem to be situated on a different origin compared to the PDB coordinates. E.g., if I: load my-structure.pdb load my-map.map, map1, 1, ccp4 isomesh msh1,map1,1.0 A nice electron density map is rendered (no errors), but offset from the my-structure.pdb coordinates (both map and coords were output from Coot where they were overlaid correctly). It sometimes works to explicitly indicate the residues around which to render the map: isomesh msh1,map1,1.0,(chain a and resi 10),carve=3.0 In my current case however, an NCS-averaged map output from Coot is not displaying at the desired location. To be clear, the map can be displayed elsewhere in space, but it does not overlap with my coordinates (these are not symmetry-generated molecules, they're part of the ASU). As Robert Campbell indicated in response to the earlier post, Pymol expects maps to be calculated to cover the whole molecule of interest. My question is why does this map/model pair display correctly in Coot while Pymol shows the map offset from the model? Is there a way to tell Pymol to place the map at a different origin (i.e. so that it overlays with the coordinates)? I realize this may also be a Coot question, but I'm not sure of the source of the problem yet so I'm posting here. I'll try the other bb if necessary. Thanks for your help, -Andy Torelli === Andrew T. Torelli Ph.D. Postdoctoral Associate Department of Chemistry Chemical Biology Baker Laboratory, Cornell University Ithaca, NY 14853 === -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] Pymol Symmetry Mates Naming
Fang, There is no relationship between ACT and PyMOL, so one wouldn't necessarily expect them to match in terms of how they name the resulting objects. However, I suspect there may also be a difference of intent: Based on a quick glance at PyMOL source code, PyMOL appears to convey a relative cell translation (based on centers of geometries), whereas ACT may be returning the computation formula. In other words, PyMOL attempts to inform the user as to whether the generated symmetry-related atom selection is within the same cell as the query selection or in one of the adjacent cells (in a translational sense). Thus in PyMOL, the (overall) nearest mates (with respect to the center of geometry) will usually have a translation of 00 00 00, and most of the time, nearby mates will vary +1 or -1 along a single translation. I'm guessing ACT simply provides the symmetry operator and the effective translation applied to generate the nearby mate. That's useful for recomputing the mate later on, but it doesn't tell the user anything about proximity. PyMOL's approach is unhelpful for recomputing a mate, but one can tell from the object name alone which objects are likely to have the most extensive contacts and how they relate in a relative sense (with respect to cell translations away from the query selection). Perhaps PyMOL could provide ACT-like naming through an optional setting? Cheers, Warren -Original Message- From: fangsh...@mbi.ucla.edu [mailto:fangsh...@mbi.ucla.edu] Sent: Thu 9/17/2009 4:52 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol Symmetry Mates Naming Hi,all, I am encountering a problem with symmetry mates generated by pymol. It seems that the naming system in pymol and ccp4-supported ACT program are not consistent. I have tested several pdbs in P4212 space group and attempted to figure out the relationship between these two, but failed. I appreciate it if you could hint me out. Some comparisons are listed below. ACT:NSYM ( number of symmetry operation) followed by number of translations of one unit cell along x,y,z. PYMOL: the first two digits are the symmetry operation. The next six digits correspond to the relative integral unit cell translation xxyyzz. I figured that the symmetry operation( the first two digits in pymol) is off by 1 compared to the first digit in ACT, but have no idea how the last six digits relates to the ACT 1em7.pdb pymolACT 0100 21-10 0200 3220 0300 4010 0500 6000 0501 6001 --- 1RH4.PDB pymol ACT 00-1100-1 03004000 010020-10 --- 178l.pdb 0100 21-10 0001 1001 03-1 401-1 07-1 8110 0700 8111 0300 4010 Sincerely Fang Sheng -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ 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] movie.roll in middle of movie
Note that this kind of stuff is much easier in PyMOL 1.2 without any scripting. (ScreenCasts for PyMOL Sponsors at http://delsci.info/id/media:new12 under Complex Movie Creation -- login first). Nevertheless, a possible answer is below: Cheers, Warren # PyMOL .pml file (tested against PyMOL 1.2) load $PYMOL_PATH/test/dat/1tii.pdb unset movie_auto_interpolate unset movie_loop mset 1 x800 zoom center,200 frame 1 mview store zoom center,50 frame 120 mview store frame 180 mview store zoom center,15 frame 280 mview store frame 360 mview store zoom center,50 frame 400 mview store frame 420 mview store mview interpolate # instead of: movie.roll 421,755 frame 531 turn y,120 mview store frame 642 turn y,120 mview store frame 756 turn y,120 mview store mview interpolate, power=1 zoom center,200 frame 800 set movie_loop mview interpolate mview smooth mplay -Original Message- From: Benjamin Bobay [mailto:ben.bo...@gmail.com] Sent: Wednesday, September 16, 2009 8:41 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] movie.roll in middle of movie Good afternoon all - I think I have a simple question. I would like to have a series of zooms followed by a movie.roll and then zooming back to the start position. Here is what I have cmd.mset(1 x800) cmd.zoom(center,200) cmd.frame(1) cmd.mview(store) cmd.zoom(center,50) cmd.frame(120) cmd.mview(store) cmd.frame(180) cmd.mview(store) cmd.zoom(center,15) cmd.frame(280) cmd.mview(store) cmd.frame(360) cmd.mview(store) cmd.zoom(center,50) cmd.frame(400) cmd.mview(store) cmd.frame(420) cmd.mview(store) cmd.movie.roll(421,755) cmd.mview(store) cmd.frame(756) cmd.mview(store) cmd.zoom(center,200) cmd.frame(800) cmd.mview(reinterpolate) The problem is that is does not do the movie.roll and as the movie plays over and over it actually performs all the zoom actions and then rotates one frame and then starts the process again from that newly rotated frame. I would like it to perform the full rotation after the initial zoom and then perform the final zoom command. Any ideas where I might have messed this up? Many thanks Ben -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] nVidia Quadro / LCD Stereo 3D Info Link
For those looking to do Quadro-based stereo 3D under Windows with the new 120 Hz LCD displays, please pay careful attention to which card you purchase if you expect to do stereo 3D! nVidia has a page with the facts you need: http://www.nvidia.com/object/quadro_pro_graphics_boards.html Good luck! Cheers, Warren -- 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] Morph Movies
Colin, Can you describe what you are trying to accomplish (overall) in more detail? There are different approaches one could take depending on the objective... The simplest, but limited approach is to use the mset and madd commands with variable numbers of frames: # show the initial state (1) for 60 frames mset 1 x60 # morph through to the final state (30) madd 1 -30 # play the final state 60 times madd 30 x60 # morph back to the initial state (1) madd 30 -1 And so on... Cheers, Warren -Original Message- From: Colin Levy [mailto:c.l...@manchester.ac.uk] Sent: Friday, September 11, 2009 11:40 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Morph Movies Hi, Anyone know how I can include a morph in the middle of a more complex movie? I have generated the morph (refine_rigimol.pdb) but cant figure how to include this set of frames into the middle of my movie. Im using Macpymol 1.2 ( generated the rigimol morph in ipymol). Many thanks Colin -- 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 -- 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] Alignment Objects
Maia, select all_arg_lys, resn arn+lys Cheers, Warren -Original Message- From: Maia Cherney [mailto:ch...@ualberta.ca] Sent: Friday, September 11, 2009 2:03 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Alignment Objects Hi, Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? Maia -- 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 -- 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] RMS
Carlos, David, etc., From the open-source code: http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/layer4/Cmd.c The returned rms values are as follows (in order): return Py_BuildValue((fiififi), rms_info.final_rms, rms_info.final_n_atom, rms_info.n_cycles_run, rms_info.initial_rms, rms_info.initial_n_atom, rms_info.raw_alignment_score, rms_info.n_residues_aligned); Cheers, Warren From: Carlos Ríos Vera [mailto:crosv...@gmail.com] Sent: Saturday, August 29, 2009 4:08 PM To: David Hall Cc: Warren DeLano; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] RMS 2009/8/29 David Hall dwash59_2...@yahoo.com pymol.cmd.align(%s % name_struct1, %s % name_struct2) oh, thanks =) should return a list, the first element of which is the rms, if I remember correctly. Warren can probably say what the rest of the elements are. On this note, maybe we could start documenting on the wiki what exactly all these commands return. It would be very useful for scripting. Yeah, it would be great get that information. -David -- http://crosvera.blogspot.com Carlos Ríos V. Estudiante de Ing. (E) en Computación e Informática. Universidad del Bío-Bío VIII Región, Chile Linux user number 425502 -- 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] Rigimol
Colin, Unfortunately, that is hard to do: there is no guarantee that the proposed (characteristic) path of motion which relates any two spacial orientations will possess reasonable chemistry or sterics. RigiMOL does make an attempt to resolve simple conflicts, and the refinement step can address minor local violations, but that is about it. The only way to work around this problem is to manually create one or more artificial intermediate conformations which do not exhibit such clashes and then morph conformation 1 to the first artificial conformation and then morph the last artificial conformation to conformation 2. That can be a lot of work, and it kind of misses the point: PyMOL (rigimol) structure morphs are only intended for visual comparison of two or more experimentally-determined structures. Molecular morphs are not (and should not be portrayed as) energetically-reasonable physiochemical paths of interconversion. To rigorously identify reasonable (low-energy) paths of interconversion, one must instead employ steered molecular dynamics or biased monte carlo simulations. Those are compute-intensive processes well beyond PyMOL's capabilities. Cheers, Warren -Original Message- From: Colin Levy [mailto:c.l...@manchester.ac.uk] Sent: Thursday, September 10, 2009 8:59 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Rigimol Hi, I have generated a morph between two large scale domain motions using Rigimol . The output is fine except that the two domains pass through each other during their trajectory. Anyone know how to avoid this type of problem. Thanks Colin -- 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 -- 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, The trick is to leave the phosphate displayed for those residues where the backbone should still be shown: hide everything, resi 20-40 and not elem p Cheers, Warren From: Bala subramanian [mailto:bala.biophys...@gmail.com] Sent: Monday, August 31, 2009 12:05 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] undisplaying residues 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 -- 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] help about mutation
Chandan, PyMOL's mutagenesis wizard is purely geometric, and is intended to offer up Dunbrack rotamers as per: http://dunbrack.fccc.edu/bbdep/bbdepdownload.php Cheers, Warren From: Chandan Choudhury [mailto:iitd...@gmail.com] Sent: Wednesday, September 09, 2009 5:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] help about mutation I am querious to know on what mathematical basis does the software mutates the amino acids. -- Chandan kumar Choudhury NCL, Pune INDIA -- 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] Creating a single PDB from two PDB - ala docking by hand
Mark, Assuming you have one of our PyMOL 1.2r1 builds (on Mac, launch as PyMOLX11Hybrid, not MacPyMOL), try the following command sequence: load $TUT/1hpv.pdb remove not (polymer or organic) remove not byres (organic expand 4) h_add flag fix, not organic show sticks, organic orient organic Now you can use the Builder to manipulate the ligand in the presence of fixed protein atoms as per my previous post (see modified excerpt below). Everyone please keep in mind that PyMOL is just a toy modeler only useful for setting up 3D poses that will be used as input for other software. If you want to do real modeling, please get Maestro, M.O.E., Sybyl, etc. Cheers, Warren Builder use: (1) activate the builder by clicking on the Builder button on the upper window (2) click the Bumps checkbox (3) click the Sculpt button Now CTRL-click-and-drag (ligand) atoms (only) around in the 3D viewer. (be careful not to click protein atoms). You'll see the little disks appear when the van der Waals radii overlap. When done, click the Clean button to minimize the structure into a nearby local minimum. NOTE: Ctrl-Z will actually undo conformational changes (ignore the Undo button for now). -Original Message- From: Mark Benson [mailto:m...@ufl.edu] Sent: Thursday, September 03, 2009 8:57 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Creating a single PDB from two PDB - ala docking by hand Dear All, I am trying to build a single PDB file from two different PDB files. One PDB has a small organic ligand, and the second PDB contains amino acid side chains from an active site. I load both PDB files, but I want to freeze the orientation of the amino acid side chains PDB ( not move it), and then place and orient the ligand PDB in a certain pose with respect to the amino acid side chains. Ideally, I would then like to save the coordinates for both the amino side chains and the ligand coordinates to a single PDB file. In the long run, I want to run a simple minimization on an possible active site cluster and I want to get a feel for the energetics of the ligand in the active site. I don't like working with MOLDEN or some of the other suites out there and I wanted to try this with PyMOL. I've gone through the manual, the web, pymolwiki, the masking and protecting options, and I've tried examining the use of frames and split_states, but I haven't come up with anything. I've heard about a demo that Warren DeLano put on for the ACS where, as part of the demo, he showed off some toy example where he docked a ligand in by hand, complete with having PyMOL show red/green dots for steric clashes/matches. Any ideas? -Mark -- 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 -- 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] Creating a single PDB from two PDB - ala docking by hand
Michael, Assuming you have a PyMOL 1.2 build with the Tcl/Tk user interface displayed: Load a small-molecule or peptide structure or simply type fab then (1) activate the builder by clicking on the Builder button on the upper window (2) click the Bumps checkbox (3) click the Sculpt button Now CTRL-click-and-drag atoms around in the 3D viewer. You'll see the little disks appear when the van der Waals radii overlap. When done, click the Clean button to minimize the structure into a nearby local energy minimum. Cheers, Warren From: Michael Lerner [mailto:mglerner+sourcefo...@gmail.com] Sent: Friday, September 04, 2009 6:15 AM To: a...@artforscience.com Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand I definitely remember some mode where PyMOL would show good/bad contacts with red/green dots, but I can't seem to figure it out now. It was in Warren's talk as he was manually docking in a ligand. I searched, but couldn't figure it out myself. Does anyone know how to put PyMOL into that mode? Cheers, -Michael On Thu, Sep 3, 2009 at 12:04 PM, H. Adam Steinberg a...@steinbergs.us wrote: Bring up both pdb files in one session, orient the ligand by going to editing mode and using the shift key with the left mouse button (3 button mouse mode) to move just the ligand. Once you have it in the position you want, type select all in the command line and then hit enter, In the A menu for the (sele) you just created pick copy to object. PyMOL will create a new pdb with all of the coordinates of the two pdb files as they are positioned on screen. Rename it if you'd like, and save the new pdb out from the File menu/save molecule. Mark Benson wrote: Dear All, I am trying to build a single PDB file from two different PDB files. One PDB has a small organic ligand, and the second PDB contains amino acid side chains from an active site. I load both PDB files, but I want to freeze the orientation of the amino acid side chains PDB ( not move it), and then place and orient the ligand PDB in a certain pose with respect to the amino acid side chains. Ideally, I would then like to save the coordinates for both the amino side chains and the ligand coordinates to a single PDB file. In the long run, I want to run a simple minimization on an possible active site cluster and I want to get a feel for the energetics of the ligand in the active site. I don't like working with MOLDEN or some of the other suites out there and I wanted to try this with PyMOL. I've gone through the manual, the web, pymolwiki, the masking and protecting options, and I've tried examining the use of frames and split_states, but I haven't come up with anything. I've heard about a demo that Warren DeLano put on for the ACS where, as part of the demo, he showed off some toy example where he docked a ligand in by hand, complete with having PyMOL show red/green dots for steric clashes/matches. Any ideas? -Mark -- 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 -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology
Re: [PyMOL] broken
Joel, When using the PyMOL launch icons, it is only possible to have one active version installed (registered) under Windows. However, you can (1) copy and rename the Program Files \ DeLano Scientific \ PyMOL folder from a correctly installed version, then (2) edit the launch.bat file inside the copied folder to point PYMOL_PATH at the copied location, and then (3) use that launch.bat to launch that copy even after removing or updating the main installed version. In such a situation, you can have one registered version and then any number of unregistered copies sitting in adjacent folders, each launchable with their own launch.bat script. If you've got a mess at present, use the Control Panel to uninstall any registered copies, then delete (or rename) the Program Files \ DeLano Scientific \ PyMOL folder (if present) and then reinstall a fresh copy of the version you wish to run. Cheers, Warren From: Joel Tyndall [mailto:joel.tynd...@otago.ac.nz] Sent: Tue 9/1/2009 4:15 PM To: pymol-users@lists.sourceforge.net Subject: [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
Re: [PyMOL] APBS in pymol1.2
Hugo, If building PyMOL from source, then please get APBS in source or binary form from the APBS sourceforge project: http://apbs.sourceforge.net Cheers, Warren -Original Message- From: Hugo G. de Teran [mailto:hugo.te...@usc.es] Sent: Thursday, August 27, 2009 10:06 AM Cc: apbs-us...@lists.sourceforge.net; pymol-users@lists.sourceforge.net Subject: [PyMOL] APBS in pymol1.2 Hi, I am trying to use APBS in pymol v1.2 (x86_64 linux compilation). I have compiled with no problem APBS, but when I try to start a calculation I get the following error: File /usr/local/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line 998, in __init__ from freemol import apbs ImportError: No module named freemol /usr/local/bin/pymol: line 2: 798 Segmentation fault /usr/bin/python /usr/local/lib64/python2.6/site-packages/pymol/__init__.py $@ I have read previous posts about freemol, but I do not want to mess up with beta-versions so I only would like to make APBS work with pymol. Thanks for help, Hugo -- Hugo G. de Teran, PhD. Parga Pondal Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hugo.te...@usc.es http://web.usc.es/~hugogdt -- 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 -- 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, Hmm...it appear that QuietException is being thrown when the input pattern fails to match any valid object name (but without an error message being printed). The easiest immediate workaround is to simply swallow the exception. for i in range(10): try: cmd.color(colors[i], sym0 + str(i) + *) except cmd.QuietException: pass Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Wednesday, August 26, 2009 4:35 PM To: pymol-users Subject: [PyMOL] Inexplicable exception raised by cmd.color() 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 -- 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] invoke ramp_new without drawing 'ramp' CGO
Stephen, ramp_new ramp-name, ... disable ramp-name Cheers, Warren -Original Message- From: Stephen Graham [mailto:steph...@strubi.ox.ac.uk] Sent: Tuesday, August 25, 2009 10:09 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] invoke ramp_new without drawing 'ramp' CGO Dear all, Is it possible to invoke ramp_new and have it not draw the 'ramp' CGO? It's easy enough to hide the CGO when working interactively, but I've yet to find a way to zap it from a script (without also getting rid of the colour ramping itself). 'hide everything, my_ramp' doesn't seem to hide the CGO, and issuing 'delete my_ramp' from within a script kills the colour ramp before it gets applied (to a surface, in this case, despite the order of operations in the script). Thanks, Stephen -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549 -- 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 -- 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] Calling scripted functions within alter_state
Hello Stuart, By default, alter_state expressions are evaluated in the pymol namespace of the current PyMOL instance, not the cmd (pymol.cmd) namespace. The reason why it works with 'run' is that run also executes in pymol by default, and thus, includes any functions you define. Try: cmd.alter_state(1, copy, x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)) instead, after using cmd.extend in your startup or GUI script. Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, August 24, 2009 3:38 PM To: pymol-users Subject: [PyMOL] Calling scripted functions within alter_state Hello Warren, all, I've been working on a plugin for PyMOLX11Hybrid, in which I have a few lines of code such as: cmd.alter_state(1, copy, x,y,z = sym_partner([x,y,z], stored.tmpOp)) AND cmd.alter_state(1, object, x,y,z = cell_shift_helper([x,y,z],stored.shift)) Both those functions (sym_partner and cell_shift_helper) are extended through cmd.extend() function, along with several others which work perfectly well. The issue arises only when I attempt to use these functions through a menu added to PyMOL GUI, which does not involve issuing the run /(filepath)/(script).py command in PyMOL, but rather initializes necessary commands on startup. I've confirmed that the cmd.extend() calls are made properly, but I can only fix the problem by issuing the run command independent of my initialization scripts. Because this script is planned to be incorporated into a build of PyMOL which will be run from a variety of file paths, I'd like to know how I can solve this problem without simply jury rigging a run command. Is there a way to properly make commands available within an alter_state command without using the run command? Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- 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] Calling scripted functions within alter_state
Stuart, Hmm...whoops, my mistake. Cmd.extend doesn't actually add a function to the cmd module -- only to the command keyword dictionary. So, instead, set it explicitly in your .py file: from pymol import cmd def my_fn(...): cmd.my_fn = my_fn # then later on, in the menu, etc.: cmd.alter_state(..., cmd.my_fn(...)) Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, August 24, 2009 4:06 PM To: Warren DeLano Cc: pymol-users Subject: Re: [PyMOL] Calling scripted functions within alter_state Hello Warren, When adding in the cmd. I get these error messages: Traceback (most recent call last): File string, line 1, in module AttributeError: 'module' object has no attribute 'sym_partner' Traceback (most recent call last): File string, line 1, in module AttributeError: 'module' object has no attribute 'cell_shift_helper' Versus the error I get with the cmd. not included: Traceback (most recent call last): File string, line 1, in module NameError: name 'sym_partner' is not defined Traceback (most recent call last): File string, line 1, in module NameError: name 'cell_shift_helper' is not defined I'm pretty stumped at this point. Does it seem like the pymol.cmd namespace isn't acquiring the new functions as it ought to be? Stuart 2009/8/24 Warren DeLano war...@delsci.com Hello Stuart, By default, alter_state expressions are evaluated in the pymol namespace of the current PyMOL instance, not the cmd (pymol.cmd) namespace. The reason why it works with 'run' is that run also executes in pymol by default, and thus, includes any functions you define. Try: cmd.alter_state(1, copy, x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)) instead, after using cmd.extend in your startup or GUI script. Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, August 24, 2009 3:38 PM To: pymol-users Subject: [PyMOL] Calling scripted functions within alter_state Hello Warren, all, I've been working on a plugin for PyMOLX11Hybrid, in which I have a few lines of code such as: cmd.alter_state(1, copy, x,y,z = sym_partner([x,y,z], stored.tmpOp)) AND cmd.alter_state(1, object, x,y,z = cell_shift_helper([x,y,z],stored.shift)) Both those functions (sym_partner and cell_shift_helper) are extended through cmd.extend() function, along with several others which work perfectly well. The issue arises only when I attempt to use these functions through a menu added to PyMOL GUI, which does not involve issuing the run /(filepath)/(script).py command in PyMOL, but rather initializes necessary commands on startup. I've confirmed that the cmd.extend() calls are made properly, but I can only fix the problem by issuing the run command independent of my initialization scripts. Because this script is planned to be incorporated into a build of PyMOL which will be run from a variety of file paths, I'd like to know how I can solve this problem without simply jury rigging a run command. Is there a way to properly make commands available within an alter_state command without using the run command? Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- 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] Zalman 3D Monitor
Joachim, I think this is more an issue of driver support rather than hardware. However, the latest drivers do not necessarily support older cards. Please see nVidia's site for details: http://www.nvidia.com/Download/index.aspx?lang=en-us and click on the supported hardware tab after searching. Cheers, Warren -Original Message- From: Joachim Reichelt [mailto:joachim.reich...@helmholtz-hzi.de] Sent: Monday, August 24, 2009 6:08 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Zalman 3D Monitor Hello, does anyone know, which Quadro card supports the Zalman mode. The readme states: Stereo options 7, 8, and 9 are only supported on G8xGL and higher GPUs. Mode 7 is for the Zalman -- Joachim -- 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 -- 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] Transparent surfaces and presets
Jose, Yes, you need to override the object-specific transparency specification from the preset: unset transparency, object-name Cheers, Warren From: Duca, Jose [mailto:jose.d...@spcorp.com] Sent: Wed 8/19/2009 10:33 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Transparent surfaces and presets Has anybody else played with presets and transparent surfaces? When I do preset - ligand site - cartoon and then try to create a surface on top of it, the surface cannot be shown as transparent; while if you try other presets surface transparency seems to work OK. Is there a reason for this behavior or is this a bug? Thanks, José * This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- Please immediately and permanently delete. -- 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] Light Command Details needed
The light and lightN settings are direction vectors, not coordinates. Intensity (reflect setting) is averaged across all such directional sources. It has recently been suggested that we need better control over lighting. Cheers, Warren -- Warren L. DeLano, Ph.D. war...@delsci.com (Sent from a mobile device. Please forgive brevity and/or typos!) On Aug 20, 2009, at 4:14 PM, Sean Moore semo...@mail.ucf.edu wrote: Hello, I could not find a way to search the archived sourceforge messages, so I apologize if this has been asked and answered. I am having trouble moving the light source before a ray command (I want to shine it into the crevice of a structure from behind and above my current view). I ended up using light, [1,5,-100]. I know these are X,Y,Z coordinates, but relative to what origin and in what units? After wasting way too much time, I concluded that the values might be Angstroms relative to the eyes of the current view. In examples I found online, the numbers are small, so this doesn't make much sense. Also, I see there are several light sources available. As more and more lights are turned on, do the XYZ values for each additional get taken in order from the top of the list? Is there a way to change the intensity of each light in addition to its position? Thanks for any help. -Sean --- --- --- - 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] Stick Radius different for selected residues, possible?
Sean, Use set_bond instead of set for per-bond properties. Cheers, Warren -- Warren L. DeLano, Ph.D. war...@delsci.com (Sent from a mobile device. Please forgive brevity and/or typos!) On Aug 20, 2009, at 4:18 PM, Sean Moore semo...@mail.ucf.edu wrote: Hello, I am trying to change the stick_radius for a few selected residues so they stand out relative to the surrounding mess of sticks. If I command, set stick_radius, 0.75, object name, the report states that the stick radius was changes for the correct number of atoms in the file, but the displayed residues all show the original value. Can the stick radius be changed for a sub-set of residues and rendered? _Sean --- --- --- - 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] coordinate transformation
Vivek, Create a copy of the original chain, modify the chain, and fit the copy to the original. For example # PyMOL 1.2 .pml input fab AAA, orig create copy, orig set_dihedral orig///3/C, orig///4/N, orig///4/CA, orig///4/C, 180 unpick fit origCA, copyCA Cheers, Warren From: Vivek Ranjan [mailto:vran...@gmail.com] Sent: Mon 8/17/2009 1:44 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] coordinate transformation Hello, I am trying to modify dihedral angles of a polymer chain. Once I perform all the required steps, I am able to orient the chain and align the chain along the same axis as the original chain. But unfortunately, pymol moves the chain to a different position. Basically, it changes the coordinates in a way that the center of the chain is at the origin. I want the chain to lie along the original chain with backbones coinciding with each other (almost). Is that possible in pymol ? -- Thank you and Regards, Vivek Ranjan -- 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 -- 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] Updated B-factor in trajectory
Oscar, Use the discrete=1 option to load each PDB state as a separate set of atoms (instead of as a trajectory -- the default behavior). load multimodel.pdb, discrete=1 Cheers, Warren From: S4C6Ar Chung [mailto:s4c...@gmail.com] Sent: Sat 8/15/2009 9:44 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Updated B-factor in trajectory Dear all, It seems to me that Pymol (v0.99) shows B-factor of the last frame only. How can I show the updated B-factor by color during trajectories. Thank you for your comment or help. Best Wishes, Oscar -- 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] AxPyMOL Updated: .MAE and .MOE support.
FYI, for Windows users who like to live on the edge... AxPyMOL is the PyMOL Active Control, which makes it possible to display live molecular content, including PyMOL PSE and PSW files inside of PowerPoint (on Windows only). Because we are still having trouble getting this Windows-based component to work perfectly (i.e. without crashing), we are continuing to give away a version of AxPyMOL as a FREE, but UNSUPPORTED extra capability for use AT YOUR OWN RISK. Today we posted an updated 1.2r1 version of AxPyMOL designed to work with PyMOL 1.2 session and show files. You can download it from: http://delsci.com/axpymol (file: axpymol-1_2r1-free-090814.msi) . Note that AxPyMOL is currently intended for use inside PowerPoint only, with external data files stored locally in the same folder as your presentation. After installation, use the Control Toolbox - More Controls button to select and drag out an AxPyMOL rectangle in your slide, and then follow the instructions shown onscreen. The PowerPoint Control Toolbox can be displayed via the PowerPoint View menu - Toolbars option. By the way, one particularly useful aspect of AxPyMOL is that it can directly read and display .MAE and .MOE files. So, if you use Chemical Computing Group's M.O.E. or Schrodinger's Maestro, then you should be able to load and interact with your .MOE and .MAE files directly inside of PowerPoint using AxPyMOL. We need more feedback on how the component works out in the real-world, so thanks in advance to those of you who try AxPyMOL and report back! Cheers, Warren PS. With Office 2007, in order to retain placeholder images, please save your presentation in .PPT not .PPTX format. -- 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] pymol autodock plugin
Jed, With the 1.2 release of PyMOL, we have completely switched over to Numpy. So the first thing to try is to replace: from Numeric import * # with from numpy import * Cheers, Warren -Original Message- From: Jed Goldstone [mailto:jedg...@mit.edu] Sent: Thursday, August 13, 2009 1:34 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol autodock plugin The autodock plugin written by Daniel Seeliger ceased to function (load) when I upgraded to Pymol 1.2r1. Although it is not compatible directly with Autodock 4, it did have the useful functionality of presenting an autodock 'box' that was readily tweakable, so that the parameters could be exported for Autodock Vina. I would LOVE to have this resurrected, but I don't know python - can anybody help with this? The specific failures I got were: File C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py, line 16, in module from Numeric import * ImportError: No module named Numeric Error: unable to initialize plugin 'autodock'. Any help would be greatly appreciated. Jed -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.mit.edu/people/jedgold/home.html (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) -- 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 -- 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] Measure surface area
Mirek, PyMOL isn't the optimal tool for measuring surface area -- perhaps others on the list can suggest good alternatives. The only kind of surface area PyMOL can measure well is solvent accessible area, and it is a bit slow because all it does is sum up partial areas associated with discrete dots on spheres (size = vdw + solvent radius). The basic approach is: # (1) make sure no atoms are ignored: flag ignore, none # (2) delete everything except what you want to measure (important!): remove not polymer # (3) adjust dot settings for solvent surface area measurement: set dot_solvent, on set dot_density, 4 # (4) visually preview what is being measured (optional): show dots # (5) computer the surface area value: print cmd.get_area() Cheers, Warren -Original Message- From: Mirek Cygler [mailto:mi...@bri.nrc.ca] Sent: Monday, August 10, 2009 11:08 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Measure surface area Hi, How can I get the measure in A2 of the surface area of the surface I display with PyMol? Mirek -- 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 -- 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] de-speculating?
Hi Tom, set specular, 0 alone should be enough to do the job if all you want to do is turn off specular lighting -- you can ignore all those other spec_* settings. However, for a more matte appearance I'd be more inclined to try: set shininess,10 set specular_intensity, 0.2 # and perhaps space pymol # in order to lessen problems with color saturation. Cheers, Warren From: Thomas Stout [mailto:tst...@exelixis.com] Sent: Friday, August 07, 2009 2:51 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] de-speculating? Hi All -- Would anyone happen to have a recipe handy for turning down/off the specularity (of CPK spheres especially) in PyMOL? I happen to be a fan of more matte surfaces and find the highlights to be rather extreme. I've been messing around with all of the parameters as found on PyMOLwiki: Spec direct Spec direct power spec power specular specular intensity as well as reflect ambient et cetera but haven't really found the sweet spot. My current settings look like: spec_count, 1 spec_direct, 0.0 spec_direct_power, 2000 spec_power, 2000 spec_reflect, 2 specular, 0 specular_intensity, 0.5 ambient, 0.08 reflect, 0.66 This is close, but loses some dimensionality in the CPK spheres (they now look flat in the middle). Oddly, the spheres look great in the GUI (unrendered) but the ray-traced version seems to clip the shading/color distribution badly Any suggestions? Thanks! -Tom This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems. -- 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] problems with apbs/pqr
James, It sounds like there mayy be something other than canonical amino acids in your structure which might need to be removed prior to performing a calculation. These may be alternate conformations of amino acid side chains, ligands, or other unrecognized groups which cannot be processed for APBS. Cheers, Warren -Original Message- From: James Whittle [mailto:whit...@mit.edu] Sent: Wed 8/5/2009 5:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] problems with apbs/pqr Hi all, My apologies if this has been covered by this list before, but I couldn't find mention of it: I'm trying to calculate an electrostatic surface for my protein. The APBS Tools plug-in crashes with the message: WARNING: 502 atoms did not have formal charges assigned WARNING: 1051 atoms did not have properties assigned This happens whether I use a pqr file from PDB2PQR or the PyMol generated PQR. I'm running OS X (Intel), Pymol version 1.2r0. I also tried it though on a linux machine, and got the same error. This plug-in works fine with several other coordinate files. I tried removing the chain ids from the pdb file, but that did not help. Can anyone offer any advice on this? --James -- 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 -- 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] PI-bond distance
I´m desperate to get some information about PyMol, I need to know it is possible to measure a distance from a middle of a pi-bond to another atom? No, this isn't possible directly, but you can do something like the following: # copy paste demo snippet load $TUT/1hpv.pdb pseudoatom pi_cent,b/53/cg+cz dist pi_centps1, b/met`46/ce Cheers, Warren Sent: Tuesday, August 04, 2009 6:03 AM To: info; sales Subject: Re: PyMol Hello, I´m desperate to get some information about PyMol, I need to know it is possible to measure a distance from a middle of a pi-bond to another atom? Hope to get answer soon as possible! Best regards, E. -- 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] Python Function with Unlimited Positional Arguments
Sean, You need a keyword argument list as well, so that the effective PyMOL class instance (_self) can be passed in by keyword (actual use of _self is only strictly required when you have multiple PyMOLs active in a single Python interpreter). # pml input: python def my_fn(*arg, **kwd): print arg cmd.extend(my_fn, my_fn) python end my_fn my_arg_1, my_arg_2 # PyMOL output: ('my_arg_1', 'my_arg_2') Cheers, Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Sunday, August 02, 2009 10:56 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Python Function with Unlimited Positional Arguments Hi PyMOLers, I am trying to write a python script that will allow a user to provide an unlimited number of positional arguments for a function. I am use to the following scheme for defining a function and its arguments: def some_function ( x, y, z, file=false): #DO SOMETHING return Where x, y, and z are required arguments and file=false is an optional argument. I came across the following page pertaining to Python: http://www.linuxtopia.org/online_books/programming_books/python_programm ing/python_ch15s09.html See Unlimited Number of Positional Arguments Values There it explains that one could use the following syntax: def some_function ( *args): print arg[0] return Now, when put this in a script and call the function in PyMOL it spits out the following error: Traceback (most recent call last): File /pymol/./modules/pymol/parser.py, line 254, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) TypeError: some_function() got an unexpected keyword argument '_self' Is the *args method simply not possible in PyMOL? I tried using **args which worked nicely for keyword arguments. Any help would be greatly appreciated. Thank you for your time. Sean Stay on top of things, check email from other accounts! Check it out. http://go.microsoft.com/?linkid=9671350 -- 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] Getting SCALE record within PyMOL
Stuart, Sorry, there is no way to do this at present (short of manually editing text files). But thank you for the suggestion! Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Saturday, July 18, 2009 1:58 PM To: pymol-users Subject: [PyMOL] Getting SCALE record within PyMOL Hello Warren, all, Is there any way to read the SCALE record from the PDB file of a protein loaded into PyMOL either within PyMOL or in a script? Alternatively, even getting the filepath from an object name so that the PDB can be accessed directly by a script would be sufficient. Thanks, Stuart Ballard -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ 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] WARNING: No Mac or Linux support for 120 Hz LCD synchronization
Just to make sure everyone understands: Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS ONLY due to the need of a special USB driver for the 3D Vision sync emitter. Unfortunately, you cannot sync a digital 120 Hz LCD using the old stereo analog DIN sync connector - it just doesn't work. Please do not waste money right now buying a 120 Hz LCD if you use Linux or Mac OS (even if you have a Quadro card), or if you use a Windows laptop (without a Quadro graphics chip). You will be disappointed -- the display will not do 3D with your system, and nVidia has not promised support for 120 Hz LCD synchronization on platforms other than Windows. That may change, but then again, it might not. Accordingly, our recommended stereo 3D solution for Mac, Linux, and for Windows systems without Quadro cards is the Zalman M220W LCD display. You get fewer pixels for stereo 3D, but it works great with PyMOL on ALL PLATFORMS (including most laptops). No special graphics hardware or drivers are required to use the Zalman with PyMOL. http://pymol.org/zalman Cheers, Warren -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ 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] WARNING: No Mac or Linux support for 120 HzLCD synchronization
Malcolm, Yes, a reasonable person might expect it to work...but we have tried on both Mac and Linux, and it doesn't work with either CystalEyes or NuVision hardware. I don't think Modeline timings have any meaning when generating a true digital display signal, but regardless, the actual sync signal output is not correct. My naïve guess is that this is because the analog sync signal from the Quadro DIN connector is based off of the SVGA vertical blanking interval and has nothing to do with the digital-only display signal required by these displays. Note that these displays do not accept an analog SVGA signal - they have only a pure-digital DVI-D connector - not DVI-I, and they have no HD15 SVGA input. They also require a full dual link DVI-D cable with all pins present. It seems that the dual-link capacity is used to carry the 120 Hz signal (perhaps split over two regions of the display? or with the left 60Hz on one channel and the right 60Hz on the other?). Furthermore, even if the Quadro sync was correct, the polarization of the old shutter glasses conflicts with that of the liquid crystal. I also observed that light from the Samsung LCD seems to interfere with the old CrystalEyes sync signal. Of course, the other problem is that affordable Quadro cards do not even come with a sync connector. So in summary, there seem to be many problems combining modern LCDs with old stereo 3D hardware, which presumably explains in part why nVidia decided to introduce a new USB emitter and glasses for use with these displays. Cheers, Warren From: Davis, Malcolm [mailto:malcolm.da...@bms.com] Sent: Friday, July 17, 2009 2:00 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] WARNING: No Mac or Linux support for 120 HzLCD synchronization Has anyone tried these with the old CrystalEyes glasses? We are looking to get one of these to try, but it is hard to understand why there should even be a need for a different graphics driver or a newer Quadro card to use it that way. The FX1100 cards we still have in some of our Linux workstations can be configured to send a 1600x1...@100hz signal to our old IBM c220p monitors and the 100Hz limit was from the monitor not the graphics card. So other than needing to specify the Modeline manually in the X config files, why shouldn't this just work? Malcolm From: Warren DeLano [mailto:war...@delsci.com] Sent: Friday, July 17, 2009 12:23 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization Just to make sure everyone understands: Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS ONLY due to the need of a special USB driver for the 3D Vision sync emitter. Unfortunately, you cannot sync a digital 120 Hz LCD using the old stereo analog DIN sync connector - it just doesn't work. Please do not waste money right now buying a 120 Hz LCD if you use Linux or Mac OS (even if you have a Quadro card), or if you use a Windows laptop (without a Quadro graphics chip). You will be disappointed -- the display will not do 3D with your system, and nVidia has not promised support for 120 Hz LCD synchronization on platforms other than Windows. That may change, but then again, it might not. Accordingly, our recommended stereo 3D solution for Mac, Linux, and for Windows systems without Quadro cards is the Zalman M220W LCD display. You get fewer pixels for stereo 3D, but it works great with PyMOL on ALL PLATFORMS (including most laptops). No special graphics hardware or drivers are required to use the Zalman with PyMOL. http://pymol.org/zalman Cheers, Warren This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ 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] WARNING: No Mac or Linux support for 120 Hz LCD synchronization .
Minor correction, for geeks who care about technical trivia. I previously wrote: I don't think [VGA] Modeline timings have any meaning when generating a true digital display signal... Apparently the modeline timings do still have significance in terms of digital information transport, which mimicks analog signal timing, but there is no hard and fast correlation between data transport and what actually happens on the screen at any moment in time. A digital display can in principle update whatever it wants, whenever it wants, once the information has arrived. Cheers, Warren -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ 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] PyMOL 1.2r1 error report
Stuart, Thank you for the reports, and sorry to hear you're having trouble. Please allow me to draw your attention to the Bug Reporter link on the PyMOL main page (www.pymol.org http://www.pymol.org/ ). The direct link is: http://sourceforge.net/tracker/?atid=104546group_id=4546func=browse One advantage of using the bug reporter system is that you can submit accompanying script or data files which reproduce the problem. With respect to meshes, rendering of meshes is not generally broken in 1.2r1, so there must be something specific about your input which is triggering the crash. We may need an example file, or at least a PDB code with associated commands, to reproduce the problem. Likewise, fetch is known not to be generally broken, so we may need more information about reproducing the problem. [For what it's worth, I just confirmed that: fetch 1fjf, async=0 show mesh ray runs fine with 1.2r1]. As for selector, it is not a supported part of the supported Python cmd API, but rather, an internal module. In other words, you should not ever need to be importing it. Operationally speaking, the Python cmd. api is defined by the file modules/pymol/api.py, and virtually all public symbols should be accessed as methods or submethods of this module. Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Thursday, July 16, 2009 2:14 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] PyMOL 1.2r1 error report Hello all, Warren, With the new PyMOL version, myself and others at the lab have found an issue with ray tracing of mesh representations causing memory utilization errors. With parameters identical to those used in previous versions of PyMOL, 1.2r1 has crashed when ray tracing isomesh generated isosurface meshes. A memory allocation error is given, but a lack of memory does not appear to be the real issue, as PyMOL crashes long before all RAM is consumed, and the same error is given when we attempt to run this process on a machine with 12GB of RAM. There have also been a few minor issues with the fetch command. Namely, we've seen intermitent inexplicable failure of the fetch command, while simultaneously using it in another version of PyMOL with no issue. Also, some older scripts now need more specific import statements to utilize certain build-in PyMOL functionality. For example, I did not need to state from pymol import selector to use the selector.process() function in other versions of PyMOL, but this is not the case with the new version. Does this reflect changes in the cmd API setup? Regards, Stuart Ballard -- Message: 1 Date: Thu, 9 Jul 2009 13:34:53 -0700 From: Warren DeLano war...@delsci.com Subject: [PyMOL] PyMOL 1.2r1 Released To: pymol-users@lists.sourceforge.net Message-ID: 896b75251ba19745a529b1b867893fa50eb...@planet.delsci.local Content-Type: text/plain; charset=us-ascii Greetings, Mac, Windows, and Linux builds for 1.2r1 were posted early this morning. Current subscribers can download them via Direct download: http://delsci.com/ip/12 or via online docs: http://delsci.info/dsc/ip As usual, I recommend caution with upgrading. Please don't upgrade right before a major talk or presentation, unless you have time to test everything thoroughly beforehand. There were many last-minute changes made after the last beta, so some glitches are to be expected. Please try loading your important PyMOL session and show files into the new version and report any serious problems. At least one additional revision of the 1.2 release is anticipated before the end of the summer. Enabling information about the new capabilities of 1.2 will be forthcoming over the next month, and will likely consist of a series of screencast demonstrations and tutorials. There is a lot of new stuff to communicate! Cheers, Warren -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists
Re: [PyMOL] 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce 3D Vision Kit
Valentina, PyMOL has been known to work great with the Samsung 2233rz for quite some time, but nVidia had not publicly released any of the required 190-series drivers until today. Note that, officially speaking, you will need a Quadro graphics card in order to do OpenGL-based stereo 3D. nVidia does not support OpenGL stereo 3D on GeForce cards, and the required control panel options for configuring OpenGL stereo 3D will be absent. More details about today's release will be posted soon... Cheers, Warren From: Valentina Corradi [mailto:valentina.corr...@gmail.com] Sent: Thursday, July 16, 2009 4:25 PM To: pymol-users@lists.sourceforge.net Subject: 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce 3D Vision Kit Dear PyMOL users, my research group is interested in using 3D stereo visualization with PyMOL. We have a Windows Vista/Linux (Fedora 11) 64 bit system, with Nvidia GeForce GTX 295 Graphic card and Nvidia GeForce 3D Vision Kit (Samsung SyncMaster 2233RZ 120Hz monitor). Dr. Delano's post, dated June 22 ( http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07014.h tml ), says that only Zalman monitor can be used with PyMOL for 3D stereo visualization. I installed the latest Nvidia 3D Vision drivers (released on June 22) officially supporting our monitor and I read on PyMOL home page that on June 30, PyMOL 1.2r0 version supports stereo 3D for Samsung display. I am wondering if now it is possible to use this PyMOL version or the latest one (1.2r1) for 3D stereo visualization together with the OS and Nvidia kit we have. Thank you in advance for your help, Valentina Corradi, University of Calgary -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ 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] Here at last: PyMOL in Stereo 3D on 120 Hz LCDs (Vista info)!
Today nVidia issued their first public beta release of their 190-series driver. Although this release is officially for GeForce hardware, it seems to work fine for Quadro cards as well. So, if you have the following hardware setup, then you can at last now use PyMOL in Stereo 3D at full 1680x1050 resolution on a 120 Hz LCD. Here is what you need: - A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm - A recent Quadro series graphics card such as an FX 380 or 570. - A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses). - Windows Vista 32 bit or 64 bit - The driver download (warning ~230 MB ZIP file): http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.htm l http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.ht ml I personally confirmed today that this download enables PyMOL to run in Stereo 3D on a 2233RZ with a Quadro 570 graphics card and GeForce 3D Vision hardware under Windows Vista 32 bit. Instructions: 1. Uninstall the existing display drivers, disconnect the USB emitter, and reboot. 2. Extract the contents of the downloaded ZIP file. 3. Run the enclosed Launch.exe, click the first option to install the graphics driver, and then reboot when prompted (essential!). 5. Again run Launch.exe, click the second option to install the 3D Vision Software, and connect the USB emitter when prompted. Confirm that the stereo 3D tests work as expected, then exit the wizard by clicking Finish. 6. Open the NVIDIA Control Panel, and increase the display refresh rate to 120 Hz using the display resolution tab. Then go to the 3D Settings tab and set the Stereo display mode to Generic active stereo (with NVIDIA IR Emitter), click Apply, and then set Stereo - enable mode to on, click Apply, and then close the NVIDIA control panel. 7. Reboot (again, essential -- OpenGL stereo 3D will not actually work until after you reboot.) 8. Launch PyMOL 1.2r1 for Windows. You should get the message: OpenGL quad-buffer stereo 3D detected and enabled. 9. Now load a PDB file and issue stereo on. The emitter should light up and the glasses should activate. Congratulations -- you should now be able to view PyMOL molecular structures in stereo 3D on a 120 Hz LCD! Cheers, Warren -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ 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] Here at last: PyMOL in Stereo 3D on 120 Hz LCDs (WinXP info)!
Continuing coverage... Although GeForce 3D Vision is not officially supported for Windows XP, I managed to get it to work with PyMOL. Assuming you have the following setup: - A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm - A recent Quadro series graphics card such as an FX 380 or 570. - A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses). - Windows XP 32 bit You need the 190-series graphics driver for Windows XP: http://www.nvidia.com/object/winxp_190.38_beta.html and the 190-series 3D Vision driver for Windows Vista: http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_190.38.html Instructions: 1. Uninstall the existing display drivers, disconnect the USB emitter, and reboot. 2. Run the Window XP graphics driver installer and reboot. 3. Launch the Vista 3D Vision driver in order to extract the files you need, but do not yet click Next on the Welcome page...just leave it open for now...do not close the installer. 4. Plug in the USB emitter. Windows should throw up the Found New Hardware Wizard**. Choose No, not this time and go to the Next page. Select install from a list or specific location and click Next to continue. Choose Search for the best driver, include this specific location..., and click Browse. Now comes the hard part: you must select the folder which contains the file nvstusb.inf. On my system, that file was unpacked into c:\Documents and Settings\Warren~1~000\Locals~1\Temp\pft16~tmp - your copy may be in a similar location. You may need to use Windows Search to find the file. Once you've chosen the correct folder, click Ok and then Next. You may then be asked to locate nvstusb.sys, which should be in the same folder. Click Ok once you've found the file, and then Finish. This should complete installation of the USB driver. **If Windows doesn't throw up the Found New Hardware Wizard, use the Device Manager to locate the device and then update the driver for the device using the same process described above. 5. Now allow the 3D Vision Installer to continue. Since your on XP, not Vista, it will complain and throw up one warning and one error message, but it should still complete. Reboot when prompted. The rest of the instructions are basically the same as for Vista: 6. Open the NVIDIA Control Panel, and increase the display refresh rate to 120 Hz using the display resolution tab. Then go to the 3D Settings tab and set the Stereo display mode to Generic active stereo (with NVIDIA IR Emitter), click Apply, and then set Stereo - enable mode to on, click Apply, and then close the NVIDIA control panel. 7. Launch PyMOL 1.2r1 for Windows. You should get the message: OpenGL quad-buffer stereo 3D detected and enabled. 8. Now load a PDB file and issue stereo on. The emitter should light up and the glasses should activate. Congratulations -- you should now be able to view PyMOL molecular structures in stereo 3D on a 120 Hz LCD using Windows XP! Cheers, Warren -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ 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] unexpected EOF while parsing
To include blocks you have to do more than indentation. You have to put a slash in front of the for statement and end all but the of the blocks with a backslash. Actually, nowadays you can just wrap Python blocks with the statements: python and python end. For example: # example pymol script an embedded Python block dele all reset python for i in range(1,10): print i cmd.pseudoatom(pos=[i,i,i],color='auto') python end zoom (all), 10 show spheres rock # use box wizard to create some walls: refresh wizard box cmd.get_wizard().set_mode(walls) wizard dele box_points turn x,-70 turn y,-30 turn z,-10 ray # end example Cheers, Warren -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Tuesday, July 07, 2009 9:16 AM To: jo...@uchicago.edu; pymol-users Subject: Re: [PyMOL] unexpected EOF while parsing Hi Jouko, You were writing a python script. Now Pymol API can handle basic Python, but it's not a one-to-one Python interpreter. To include blocks you have to do more than indentation. You have to put a slash in front of the for statement and end all but the of the blocks with a backslash. When trying to do programming, better stick to Python. Save the following as script.py and use run script.py from within Pymol or just issue 'pymol script.py': from pymol import cmd z=-7.653 inc=0.5 Sections=100 FirstToLast=range(100) for j in FirstToLast: pdb=/home/jouko/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_ + str(z) + .pdb cmd.load(pdb) cmd.do(@/home/jouko/b_color8.plm) cmd.png(pdb+.png) cmd.delete(pdb) z=z+inc print z ### Cheers, Tsjerk On Tue, Jul 7, 2009 at 5:47 PM, jo...@uchicago.edu wrote: Thanks to you and Gregori Gerebtzoff, I can now load the pdb, color the image, and save it as a picture. However I can only do that for the first cross section. I am still getting the unexpected EOF error. I did have the line indented after the loop. I think that maybe when I copied and pasted the script to the email the tab was lost, so this time I am adding the script file as an attachment. Thanks, Jouko P.S. I found that @/home/jouko/b_color8.plm and cmd.do(@/home/jouko/b_color8.plm) both work. Original message Date: Tue, 7 Jul 2009 09:17:53 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [PyMOL] unexpected EOF while parsing To: jo...@uchicago.edu Cc: pymol-users@lists.sourceforge.net Hi Jouko, I think you went through the Python and Pymol tutorials a bit too fast ;) You're writing a Python script to be loaded with 'run'. That means you have to adhere to Python API and can't use the Pymol specific language. E.g. you can't use 'png pdb', but have to use 'cmd.png(pdb)' in which case pdb will be treated as a variable rather than a string. And you definitely can't use '@something.pml'. The EOF is because you violated one of the basic rules of Python: it uses indentation to structure programming. Thus after a for loop you have to start an indented line. Furthermore: - range by default starts from 0: range(0,Sections) is equal to range(Sections) - load will strip .pdb from the filename, so you wouldn't be able to use the variable pdb to point to it; better specify a name - png probably adds .png to the name, but it's good to make sure it does ### from pymol.cgo import * import colorsys,sys,re from pymol import cmd z=-8.153 inc=0.5 Sections=100 for j in range(0, Sections): pdb=c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2- 4a/DensityCube_Lysozyme2-4a_+ str(z) + .pdb load(pdb,pdb) cmd.do(@c:/b_color8.plm) cmd.png(pdb+.png) cmd.delete(pdb) z=z+inc Hope it helps, Tsjerk On Tue, Jul 7, 2009 at 3:17 AM, jo...@uchicago.edu wrote: I am new to pymol and python. I have a number of cross sections of lysozyme. I want to display them one by one, color them using a script file that I have written earlier, and save the image. I have written a script file that I had hoped would do this. I have a couple problems with script file, but the one that is frustrating me the most is that immediately after the beginning of for loop pymol says that there in an unexpected EOF. The other problem is that when I try to use the variable pdb, pymol does not use the value of the variable, but the variable name itself. I have pasted my script file below and part of the log file. from pymol.cgo import * import colorsys,sys,re from pymol import cmd z=-8.153 inc=0.5 Sections=100 for j in range(0, Sections): pdb=c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2- 4a/DensityCube_Lysozyme2-4a_ + str(z) + .pdb load pdb �...@c:/b_color8.plm png pdb delete pdb z=z+inc PyMOL@c:/Users/jouko/CrossSections.plm PyMOLfrom pymol.cgo import *
Re: [PyMOL] subversion revision for 1.2?
Michael, Sorry for the confusion: Although 32-bit 1.2r0 Windows and Linux builds have been announced, Mac builds, 64-bit Windows Linux builds, as well as final updates to the open-source code build scripts are still in process. Once the complete 1.2 release is ready, that fact will be announced on pymol.org. Cheers, Warren -Original Message- From: Michael Banck [mailto:mba...@debian.org] Sent: Sat 7/4/2009 7:37 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] subversion revision for 1.2? Hi, maybe I missed it in the announcement, but what is the subversion revision for 1.2? I can't find a tag in the repo, nor any obvious commit message. Thanks, Michael -- ___ 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-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] DCD Trajectories and Movie Panel
Sean, The movie panel operates on movie frames, not trajectory states, so you need to create a relationship between them. A one-to-one relationship can be created using the Python command: cmd.mset(1 -%d % cmd.count_states()) Or alternatively, you can use the new Movie - Program - State Loop or State Sweep menu items. Cheers, Warren -Original Message- From: Sean Law [mailto:magic...@hotmail.com] Sent: Thu 7/2/2009 7:12 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] DCD Trajectories and Movie Panel Hi all, I am playing around with the new PyMOL 1.2 release and was hoping to use the Movie Panel in conjunction with a loaded DCD trajectory file. However, after loading the MD trajectory and setting movie_panel to 1 I don't see the prescribed time line below the viewing area. Of course, if I add a camera loop then the movie panel appears. Is this a potential use for the movie panel or is this functionality not available yet? Thank you for your time. Sean _ Create a cool, new character for your Windows LiveT Messenger. http://go.microsoft.com/?linkid=9656621 -- ___ 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] ZM-M220W and TRIMON ZM-M220W
The difference? $769.99 - $354.99 = $415 exactly. But seriously, this is a question for Dell, not pymol-users. For what it is worth, mid $300's is the current per-unit pricing for the ZM-M220W display - but they originally hit the market at a 2-3X higher price, so one of those links is probably old. Cheers, Warren From: Lihua Wang [mailto:mole...@gmail.com] Sent: Tuesday, June 30, 2009 11:44 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] ZM-M220W and TRIMON ZM-M220W Hi PyMOL users: I am looking into stereo 3D on LCD monitors. What is the difference between ZM-M220W and TRIMON ZM-M220W? http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx? c=usl=ens=hiedcs=RC956904sku=A2550610 http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx ?c=usl=ens=hiedcs=RC956904sku=A2550610 and http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx? c=usl=ens=hiedcs=RC956904sku=A1997135 http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx ?c=usl=ens=hiedcs=RC956904sku=A1997135 Thanks! -- ___ 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] Your Mom is Open Source (Fun stuff -- hey, it's Friday!)
Have you heard? You Mom Is Open Source! http://winkleman.com/exhibition/view/1628 No, that is not some veiled condemnation of maternal virtue, but rather the provocative title of Shane Hope http://www.shanehope.info 's latest Solo Exhibition at the Winkleman Gallery http://www.winkleman.com in New York City. Shane is a modern artist (a digital surrealist?) who applies PyMOL and other open-source tools as traditional artists employ pencil or paintbrush. Not to be missed from his current expo are two works with familiar titles for PyMOL users: ray_trace_mode=2 http://winkleman.com/artist/seriesworkview/1406/376/10324/2 and cartoon_trace_atoms=1 http://winkleman.com/artist/seriesworkview/1406/376/10326/2 though my personal favorite is his Junk DNA Sculptural Ontogenesis http://winkleman.com/artist/seriesworkview/1406/376/10327 Shane's other recent mol mods can be browsed http://winkleman.com/artist/seriesview/1406/376 online. Congratulations to Shane Hope on this latest exhibition! Cheers, Warren http://shanehope.info http://shanehope.info/ http://www.winkleman.com http://www.winkleman.com/ -- ___ 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] is font_color universal?
Tom, # per-object: set label-color, color-name, object-name # per-atom: set label-color, color-name, selection # for example fragment arg label all, name set label_color, yellow, arg set label_color, red, elem c # note that the other label settings may not work below the per-object level Cheers, Warren From: Thomas Stout [mailto:tst...@exelixis.com] Sent: Wednesday, June 24, 2009 10:59 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] is font_color universal? Hi All -- In my reading of the documentation/wiki and experimenting with settings, it looks like font_color is universal, meaning that you can only have one font color for ALL objects in a session file -- correct? I was hoping to have different color labels for different objects, so if anybody knows how to manage that (without resorting to Photo$hop), I'd be very interested to hear! (I'd like the labels to be the same color as the alpha-Carbon to which they are attached) Cheers, Tom -- ___ 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] Caution - 120 Hz LCDs: Not CRT killers yet...
Hari Others, At this moment, the LCD flat panel to buy for use with PyMOL is the Zalman M220W (scan-line interleaved, passive stereo 3D). Unfortunately, last week's nVidia driver updates do not contain the expected support for 120 Hz LCDs from Samsung and ViewSonic. However, my personal belief and conviction is that they will be supported in the near future, and that they will work with PyMOL -- at least under Windows XP and Vista. Furthermore, having personally tested the stereo 3D capabilities of both the Samsung and ViewSonic displays with nVidia 3D Vision emitter and glasses, the Samsung 2233RZ is so much better at generating a clean, nearly ghost-free stereo 3D effect, that I plan to strongly recommend the Samsung 2233RZ over the ViewSonic VX2265wm, if (when) nVidia releases their stereo-3D-capable OpenGL drivers for 120Hz LCDs. Whereas the Samsung's 3D effect is equal to, if not better than a CRT, the ViewSonic is clearly inferior to both -- at least in my experience, using nVidia 3D Vision glasses. Hopefully ViewSonic's future 120 Hz products will be more competitive! So recap: If you need stereo 3D-capable today, then buy a Zalman M220W http://pymol.org/zalman . That display will work with Mac, Windows, and Linux, without need of any special graphics card. You give up half the vertical resolution, but hey -- it works today, and it works quite well. However, if you expect to need a stereo 3D capable LCD in the future, then plan on buying a 120Hz Samsung 2233RZ with the nVidia 3D Vision glasses and an updated Quadro graphics card. This will give you same high-quality, full-resolution 3D effect as a Crystal Eyes-based CRT setup. But please do wait until the critical drivers are released before spending any money, and realize that you may be stuck using Windows for the time being. Cheers, Warren -Original Message- From: hari jayaram [mailto:hari...@gmail.com] Sent: Monday, June 22, 2009 7:16 AM To: PyMOL-users@lists.sourceforge.net; c...@jiscmail.ac.uk Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet... Hi I am wondering if there is a linux nvidia driver update or any other hack that allows Crystal Eyes 3 stereo products to work with the LCD 120Hz flat panel monitors. I should have read Warrens warning post (Dated Jan 23 , 2009 [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet) , before purchasing the Viewsonic VX2265wm 120Hz LCD. But my CRT died last week and since I was addicted to pymol/coot-in stereo ( with Crystal Eyes 3 ) , I rushed out and bought this 120 Hz LCD monitor. Of course things dont work . And I am wondering if there is any update from nvidia or any other workaround that allows me to get stereo on this setup. Monitor : Viewsonic FuHzion VX2265wm 120Hz Graphics card: Quadro FX 4600 OS: Ubuntu Linux X86_64 - Hardy Heron 8.04 Stereo glasses: Crystal Eyes 3 with 3pin mini din connector Thanks for your help in advance Hari Jayaram Brandeis University On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano war...@delsci.com wrote: Donnie, This tripped me up for a while too, but I think the stereo DIN is an output (for projector, Z-screens, etc.) not an input. Suffice it to say that the nVidia USB dongle does not work (in my hands, with or without USB power) as a VESA-based emitter the way we apparently both hoped it would! Cheers, Warren -Original Message- From: Donnie Berkholz [mailto:dberkh...@gentoo.org] Sent: Tuesday, February 10, 2009 9:49 AM To: Warren DeLano Cc: PyMOL-users@lists.sourceforge.net Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet... On 23:26 Thu 22 Jan , Warren DeLano wrote: I tested out the Samsung Syncmaster 2233RZ / NVIDIA 3D Vision bundle today ($599 for a 120 Hz LCD display with one pair of glasses). I was very much hoping that this new display would nevertheless also work with existing nVidia Quadro-based Mac or Linux systems with existing emitters and glasses running existing OpenGL software. Sadly, this does not seem to be the case due at least in part to the fact that the phase of the sync signal coming out of the Quadro card does not match the update phase of the LCD display. In addition, light from the display itself seems to corrupt the sync signal for StereoGraphics glasses. Hi Warren, Did you happen to try the new glasses + emitter with a CRT? I am particularly curious whether this works on Linux, or whether it needs some sort of USB driver stubs so that Linux knows what to do with these devices. It comes with a stereo-DIN cable so it seems like it could work, provided the emitter can get power via USB and the glasses can charge via USB. If the new glasses can work with a CRT, then at least we could buy stereo bundles now and use
Re: [PyMOL] Animation/ Matrix Question
Zach, Can you wait a week or two? This sort of thing is about to get 100X easier in PyMOL... Cheers, Warren -Original Message- From: Charlop-Powers, Zachary [mailto:zachary.charlop-pow...@mssm.edu] Sent: Thu 6/18/2009 10:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Animation/ Matrix Question Hi, I would like to create a movie where my molecules are moving at the same time that the camera is moving in/around/though them. I have been using Slerpy to get the movement effects that i would like but I would also like to make the molecules undergo translation/rotation functions relative to one another. Slerpy also has this capability but limited for what I would like to do. Using the Slerpy 'saction' command I can have the option to change elements in the scene but then Slerpy will interpolate 50 frames until the next shot and I don't get to coordinate my molecular movements with my camera movements. I can approach this if I shorten the default frame number in slerpy (take steps of 5 or something like that) but then I don't get to take advantage of Slerpy's smooth camera motion. Although there may be many ways to do what I would like to do, does anyone have any experience with outputting the view matrix (get_view) for each of slerpy's camera positions? If so, I could do a dry run with Slerpy, use get_view to output the view matrix and then combine each view with a rotate/translate function in order to get the effect I am looking for. The only problem is that I haven't figured out how to do that. Perhaps someone on this list already has? Hmmm. I think the most logical way would be if there were some script that could get_view for each frame of the final movie. Any help/suggestions would be greatly appreciated. best, zach cp Thank You Warren; Pymol is a great program and the PyMolWiki has become a fantastic resource for newbies. -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects___ 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] Disabling cartoon_highlight_color
set cartoon_highlight_color, default From: Roger Rowlett [mailto:rrowl...@mail.colgate.edu] Sent: Thursday, June 11, 2009 7:17 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Disabling cartoon_highlight_color How do you disable cartoon_highlight_color once it has been enabled? The command set cartoon_highlight_color, off does not work in 1.2b3, as suggested by the Pymol wiki. Pymol just reports that off is not a color. Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects___ 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] How to plot residu with a number 9999
Stephane, Okay, I see -- you're just spilling the top digit into the chain id. So for residue 10123, you can issue a selection like: zoom chain 1 and resi 0123 Looking over the code, I note that PyMOL has a hardcoded resi field of just four characters plus a null. Given how C compilers pack structs, I suspect we could extend that to 7 characters plus a null without adversely impacting PyMOL's memory use characteristics... Cheers, Warren -Original Message- From: ABEL Stephane 175950 [mailto:stephane.a...@cea.fr] Sent: Tuesday, June 09, 2009 12:34 AM To: Warren DeLano Subject: RE : [PyMOL] How to plot residu with a number Warren, Thank you for your response Indeed, you are right and this is a well known limitation of the pdb format. But as you can see with the file i join in this message obtained from a molecular dynamics software, you can also use the field 22 - 26 to extend the resSeq to 9 and this with pymol and rasmol. -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com -- Message d'origine De: Warren DeLano [mailto:war...@delsci.com] Date: mar. 09/06/2009 02:01 À: ABEL Stephane 175950; pymol-users@lists.sourceforge.net Objet : RE: [PyMOL] How to plot residu with a number Stephane, As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB residue identifier field is only four characters wide. So how could you possibly have a PDB file with residue identifiers larger than ? Cheers, Warren -Original Message- From: Stephane Abel [mailto:stephane.a...@cea.fr] Sent: Monday, June 08, 2009 7:30 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to plot residu with a number Hi pymol users It seems that the command select, residue xxx to plot residue xxx where xxx is greater than does not work in pymol version 0.99rc6 Indeed for a pdb file with ~ 13800 residue, if i use the command: select water1846, residue 1846 - the water molecule with the residue number 1846 is plotting But when i use the same command (say select water11100, residue 11100) for plotting the residue 11100 the previous command does not work How to tackle this problem. Thanks in advance for your help Stephane -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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] How to plot residu with a number 9999
Whoops, I misread my own code: In fact, PyMOL already supports 5-character residue identifiers! Here's how you use them, assuming a PDB file where the resi field spills into chain: load your_file.pdb alter all, resi=chain+resi sort # and off you go indicate resi 1: zoom resi 10123 Cheers, Warren -Original Message- From: Warren DeLano Sent: Tuesday, June 09, 2009 12:26 PM To: ABEL Stephane 175950 Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to plot residu with a number Stephane, Okay, I see -- you're just spilling the top digit into the chain id. So for residue 10123, you can issue a selection like: zoom chain 1 and resi 0123 Looking over the code, I note that PyMOL has a hardcoded resi field of just four characters plus a null. Given how C compilers pack structs, I suspect we could extend that to 7 characters plus a null without adversely impacting PyMOL's memory use characteristics... Cheers, Warren -Original Message- From: ABEL Stephane 175950 [mailto:stephane.a...@cea.fr] Sent: Tuesday, June 09, 2009 12:34 AM To: Warren DeLano Subject: RE : [PyMOL] How to plot residu with a number Warren, Thank you for your response Indeed, you are right and this is a well known limitation of the pdb format. But as you can see with the file i join in this message obtained from a molecular dynamics software, you can also use the field 22 - 26 to extend the resSeq to 9 and this with pymol and rasmol. -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com -- Message d'origine De: Warren DeLano [mailto:war...@delsci.com] Date: mar. 09/06/2009 02:01 À: ABEL Stephane 175950; pymol-users@lists.sourceforge.net Objet : RE: [PyMOL] How to plot residu with a number Stephane, As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB residue identifier field is only four characters wide. So how could you possibly have a PDB file with residue identifiers larger than ? Cheers, Warren -Original Message- From: Stephane Abel [mailto:stephane.a...@cea.fr] Sent: Monday, June 08, 2009 7:30 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to plot residu with a number Hi pymol users It seems that the command select, residue xxx to plot residue xxx where xxx is greater than does not work in pymol version 0.99rc6 Indeed for a pdb file with ~ 13800 residue, if i use the command: select water1846, residue 1846 - the water molecule with the residue number 1846 is plotting But when i use the same command (say select water11100, residue 11100) for plotting the residue 11100 the previous command does not work How to tackle this problem. Thanks in advance for your help Stephane -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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] Distinct labels on white background (ray tracing)? (JimRemington)
Sorry, I accidentally forgot to CC the list on my response to Jim. Yes, the culprist is one of the 600+ settings (ray_label_specular to be exact). Recipe for jet-black labels below... fragment methane zoom label all, name bg white unset depth_cue unset ray_label_specular set label_color, black set label_font_id, 7 set label_size, 30 ray Cheers, Warren -Original Message- From: Jason Vertrees [mailto:j...@cs.dartmouth.edu] Sent: Monday, June 08, 2009 5:12 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Distinct labels on white background (ray tracing)? (JimRemington) Message: 1 Date: Wed, 03 Jun 2009 13:52:25 -0700 From: Jim Remington reming...@molbio.uoregon.edu Subject: [PyMOL] Distinct labels on white background (ray tracing)? To: pymol-users@lists.sourceforge.net Message-ID: 4a26e289.3040...@molbio.uoregon.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed I would like to have distinct labels for hydrogen bond lengths on a ball-and-stick image with white background (as required for publication in a particular journal). No matter what I do, the labels come out washed out and usually light grey. This includes experimenting with label color, size and font (is there a bold font?). For the record, I've tried the clues in the wiki and forum, for example I've turned off ray-trace-fog, depth cueing, ray-shadowing and very high resolution images. I still get light grey labels on white background. Does anyone have further suggestions? Thanks much, Jim Jim, I can also reproduce this. I think it's either a bug or one of the 600 settings has a default that is throwing this off. If you need this ASAP and don't mind the extra steps, here's a workaround. You make two photos and composite them. Here's how (with comments): # prepare the scene; and hide your labels set ray_opaque_background, 1; bg_color white; hide labels; # set up your scene ray trace it png layer1.png, ray=1, height=yourSize, width=yourWidth, dpi=yourDPI # now hide everything but the labels and ray trace the scene # in mode3--which does make black labels: set ray_opaque_background 0; hide; show labels; set ray_trace_mode, 3; # do NOT move the scene in any way; ray trace it png layer2.png, ray=1, height=yourSize, width=yourWidth, dpi=yourDPI # go into the GIMP or Photoshop and composite the images # (put layer2 on top of layer1) or if you have ImageMagick system composite layer2.png layer1.png finalImage.png # [optional] Send me $50. :-) To get an idea of compositing, check out the 2nd example image/script from: http://www.pymolwiki.org/index.php/Gallery Lastly, Warren I'm sure has a one-line answer, but this should get you going. HTH, -- Jason -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org/ -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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] map smaller than in Coot
Greetings Michael, I suspect this is a question PyMOL automatically normalizing the map values, whereas the other programs might not. For historical reasons, PyMOL's default behavior is to normalize CCP4 map values upon loading. To prevent this, issue: unset normalize_ccp4_maps before loading the map file. Cheers, Warren -Original Message- From: Michael Oldham [mailto:mlold...@purdue.edu] Sent: Monday, June 08, 2009 1:18 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] map smaller than in Coot I have a map that I generated from VOIDOO for a cavity in my protein structure. In Coot and O it shows up as the same size and fully covers a ligand visible in my structure. In PyMol it is visibly smaller and does not cover the ligand as well. does anyone have any idea of a parameter that can be changed to show the map as it looks in Coot. Thanks -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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] How to plot residu with a number 9999
Stephane, As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB residue identifier field is only four characters wide. So how could you possibly have a PDB file with residue identifiers larger than ? Cheers, Warren -Original Message- From: Stephane Abel [mailto:stephane.a...@cea.fr] Sent: Monday, June 08, 2009 7:30 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to plot residu with a number Hi pymol users It seems that the command select, residue xxx to plot residue xxx where xxx is greater than does not work in pymol version 0.99rc6 Indeed for a pdb file with ~ 13800 residue, if i use the command: select water1846, residue 1846 - the water molecule with the residue number 1846 is plotting But when i use the same command (say select water11100, residue 11100) for plotting the residue 11100 the previous command does not work How to tackle this problem. Thanks in advance for your help Stephane -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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] Hi all...
As for the your general question: can you import pymol; from pymol import cmd; pymol.finish_launching(); etc? Answer 1: Yes, if you manually compile PyMOL open-source code into an existing Python interpreter. Or Answer 2: Yes, if you run your Python script using PyMOL's built-in Python interpreter (launch PyMOL as follows): ./pymol your-script.py # with full 3D GUI ./pymol -qc your-script.py # command-line only (in a terminal) Or Answer 3: Yes, if you call your Python script from a PyMOL script via the run or spawn commands inside PyMOL. However, Answer 4: No, if you want precompiled PyMOL build to work with an external precompiled Python build. This approach has proved impractical due unavoidable application binary interface (ABI) version mismatches between PyMOL, Python, and the host environment. As for your specific question, this is something you could do with a plain old script without even introducing the complexity of Python: load $TUT/1hpv.pdb, query remove not polymer create tmp, query set dot_solvent get_area tmp, load_b=1 # threshold on what one considers an exposed atom (in A**2): remove tmp and b2.5 tmp_dict = {} iterate tmp, tmp_dict[(chain,resv)]=1 select exposed exposed = tmp_dict.keys() exposed.sort() print Solvent exposed residues (chain,residue): for res in exposed: print res select exposed, query in tmp dele tmp # visual confirmation color white color red, byres exposed set sphere_solvent as spheres orient Cheers, Warren -Original Message- From: Yasser Almeida Hernandez [mailto:pedro...@fenhi.uh.cu] Sent: Friday, June 05, 2009 9:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Hi all... I want to make a python script to list the surface residues of a protein. The idea is import the pymol module inside the script, receive the pdb file to be analyzed and run the pymol's commands to do this task. It is possible..? the script is to tun in a classical terminal... Thanks... Correo FENHI -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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] Principal Axes of Rotation
Sean, orient selection followed by a 90 degree rotation about the camera's ]X-axis should give you a couple of views with the desired characteristics. turn x, 90 Cheers, Warren From: gilleain torrance [mailto:gilleain.torra...@gmail.com] Sent: Wed 6/3/2009 5:02 AM To: pymol-users Subject: Re: [PyMOL] Principal Axes of Rotation Hi, I might be wrong, but might it be that you need the axis through the structure that minimises the distance of all the points to it. Or, to put it another way, the least-square-plane through the structure, the normal to that plane, and a thir axis perpendicular to both. If this is the case, you are in luck, as I already made such a thing: http://pymolwiki.org/index.php/Bounding_Box this script was designed to make a minimal bounding box (not just an axis-aligned one). I think that it does this, although my geometry is not good enough to know if I am right. Anyway, you already mention joining opposite faces of the box - well just use the axes calculated half-way through the first function. Hope this helps. gilleain On Tue, Jun 2, 2009 at 11:41 PM, Sean Law magic...@hotmail.com wrote: Hi, For the past couple of days I've been trying to find a way to rotate an object in order to show a front and side profile for publication. However, rotating with respect to the x, y, or z axes does not produce the correct result (even after moving the center-of-mass of the structure to the origin). What I need is a way to determine the principal axes of rotation for a given selection so that rotation about any one of these axes does not produce a wobble effect. I've even tried drawing a rectangular box around the object and then drawing an axes through the centroids of opposing faces but I still see wobbling. I've basically exhausted all of my attempts at this problem. Any help or suggestions would be greatly appreciated. Sean Create a cool, new character for your Windows Live(tm) Messenger. Check it out -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get___ 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] Principal Axes of Rotation
Sean, Apologies for not understanding... You definitely need orthoscopic, but there's more to it. set orthoscopic fetch 1bna, async=0 orient 1bna cmd.matrix_copy(None,1bna) reset from chempy.cpv import average cmd.origin(position=average(*cmd.get_extent())) center origin # now, the maximum extent in the X Y planes should be invariant to 180 degree rotations about the Y or X axes respectively. Cheers, Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Wed 6/3/2009 12:28 PM To: matthew.frank...@imclone.com Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Principal Axes of Rotation Matt, Unfortunately, as a somewhat experienced PyMOL user, I already have orthoscopic view turned off (along with depth cue turned off). Thanks for your suggestion though. Sean Subject: Re: [PyMOL] Principal Axes of Rotation To: magic...@hotmail.com CC: pymol-users@lists.sourceforge.net From: matthew.frank...@imclone.com Date: Wed, 3 Jun 2009 15:13:25 -0400 Sean Law magic...@hotmail.com wrote on 06/03/2009 12:52:45 PM: Warren, After a deja vu moment, I realized that I had posed a similar question to you before about this (although, we didn't really have a resolution then). I had already tried your suggestion before I had posted to the mailing list but perhaps an example would be more appropriate in terms of what I'm seeing. (snip - 180 degree rotation around x axis) 7) You will now see that after 2 turns that the O3' atom is situated well past the vertical (imaginary) line drawn by the position of your cursor on your screen This is almost certainly due to the perspective view which is on by default. As atoms move closer to your viewpoint, they appear bigger, and the inter-atomic distances also appear bigger, just as in real life. So, an atom which is far away and at a particular (apparent) x position, will be farther away from the center of the screen once you've done your 180 degree rotation. This drawing mode was created to make structures look more realistic. If you don't like it, you can turn it off: under Display, choose Orthoscopic view. That should eliminate your wobble effect. 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. Attention all humans. We are your photos. Free us. http://go.microsoft.com/?linkid=9666044 -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get___ 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] reorienting a chain
Vivek, Please see the example I posted today for Sean Law -- the cmd.matrix_copy command embedded therein (followed by reset) performs exactly the action you're looking for. Cheers, Warren From: Vivek Ranjan [mailto:vran...@gmail.com] Sent: Wed 6/3/2009 9:26 AM To: Warren DeLano Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] reorienting a chain Hello Warren, Thank you very much for your advice. I guess I was not being very clear. what i meant was that i would also like to save the coordinates of this reoriented polymer. Let me be clear: I have a polymer aligned along y-axis. I change some of the dihedral angles. As a result, the chain is pointing in some arbitrary direction. So, I want to re-orient the polymer along the y-axis and then save the coordinates of this reoriented polymer. I used the command orient from the installed pymol on my system (version 1.0r2). But when I try to save the polymer, it still saves the same coordinates as the one before reorientation. Please let me know if something can be done ? Thank you, Vivek On Tue, Jun 2, 2009 at 8:50 PM, Warren DeLano war...@delsci.com wrote: You can save a copy of the original and then superimpose the copy back onto it # using fab command from the latest 1.2 beta to create poly-ala fab AAA, pol # create copy of the polymer create copy, pol # adjust a torsion set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60 # superimpose back on the original copy fit pol, copy Cheers, Warren From: Vivek Ranjan [mailto:vran...@gmail.com] Sent: Tue 6/2/2009 10:57 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] reorienting a chain Hello, I have a long chain of polymer. Once I change some dihedral angles, it orients in a different direction. I would like the chain to be reoriented in the same direction as it initially was. Is it possible within pymol ? How can I achieve this ? -- Thank you and Regards, Vivek Ranjan -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- Thank you and Regards, Vivek Ranjan -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get___ 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] Selection/remove bug?
Hi Jim, B all by itself is a selection language keyword for the b-factor property: select high_b_factor, b 50 So just use a different selection name: select chB, chain B Cheers, Warren From: Jim Remington [mailto:reming...@molbio.uoregon.edu] Sent: Tue 6/2/2009 2:08 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Selection/remove bug? Dear All: One of our crystals contains a dimer in the asymmetric unit, with chains labeled A and B. If I want to display chain b, I can first select chain a and remove the atoms, using the commands: select a, chain a ( (a) action menu: remove atoms) Result: atoms removed However, if after beginning anew or otherwise, I want to display chain a, the same commands fail. select b, chain b ( (b) action menu: remove atoms) Result: Selector-Error: Malformed selection. ( b )-- Any advice would be appreciated! Thanks, Jim -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get___ 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] reorienting a chain
You can save a copy of the original and then superimpose the copy back onto it # using fab command from the latest 1.2 beta to create poly-ala fab AAA, pol # create copy of the polymer create copy, pol # adjust a torsion set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60 # superimpose back on the original copy fit pol, copy Cheers, Warren From: Vivek Ranjan [mailto:vran...@gmail.com] Sent: Tue 6/2/2009 10:57 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] reorienting a chain Hello, I have a long chain of polymer. Once I change some dihedral angles, it orients in a different direction. I would like the chain to be reoriented in the same direction as it initially was. Is it possible within pymol ? How can I achieve this ? -- Thank you and Regards, Vivek Ranjan -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get___ 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] wrl and dx files problem
Raluca, PyMOL transforms the output geometry in order to deliver a default view matching what's seen in the viewer window. To prevent that, you'll need to effectively eliminate PyMOL's camera transformation by restoring to a transformation-less identity matrix: cmd.reset() cmd.origin(position=[0,0,0]) cmd.center(origin) cmd.move('z',-cmd.get_view()[11]) At this point, there may not be anything visible in the viewer window, but the output WRL file will have the same coordinate system as the input PDB, DX map, etc. Cheers, Warren From: Raluca Mihaela ANDREI [mailto:r.and...@sns.it] Sent: Fri 5/22/2009 10:51 AM To: pymol-users Subject: [PyMOL] wrl and dx files problem Hello! I save the surface of a protein as a .wrl, then I calculate the electrostatic potential and I save again the surface of the protein. I import the two surfaces in Blender (a 3D software) and I see that they are shifted. Why does this happen? Then I open the .wrl files and the .dx file in another home made program and I see that the surfaces and the grid have not the same origin. Can somebody tell me why the surface and the grid don't have the same origin and what do I have to do in order to fix this? Thank you, Raluca -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get___ 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] update mesh level to custom value after deleting map object
Hari, isolevel mesh-name, level Cheers, Warren From: hari jayaram [mailto:hari...@gmail.com] Sent: Wednesday, May 27, 2009 12:29 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] update mesh level to custom value after deleting map object H I have an old pymol session file . I have a mesh object displayed whose level I can manipulate in predetermined ways using the Action-Level-menu. I however want to pick a level different from the menu options provided . A further complication is that I have deleted the original map object and want to avoid going looking for it. Is there a way to pick a level for a mesh object that is not pre-programmed into the Action menu . Thanks Hari -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___ 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] Load Selection
Sean, You can save some time a lot of memory by loading the file and removing the atoms in a single-line compound statement (with a semicolon after the load statement). load 1E3M.pdb; remove not A-C+F// Cheers, Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Tuesday, May 26, 2009 9:10 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Load Selection Hi PyMOLers, I was wondering if there is a way to load part of a PDB file if you know a priori what you want thereby saving time/memory? Currently, I have a system that is ~160,000 atoms (protein-DNA complex with explicit water molecules taken from an MD simulation). When I load more than 10 structures I start running out of memory so I was hoping that there was some way that I could specify on the command line to only load the protein/DNA but not the water. Right now, I have to pre-process each pdb file before loading which seems tedious. I was hoping that there was already some built-in function in PyMOL that can handle this immediately by invoking something like: load 1E3M.pdb, selection=c. a+b or c. e+f Thank you for your time. Sean Create a cool, new character for your Windows Live(tm) Messenger. Check it out http://go.microsoft.com/?linkid=9656621 -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] surface of ligand
set surface_mode, 1 Cheers, Warren -Original Message- From: chaix denis [mailto:ch...@cbs.cnrs.fr] Sent: Tuesday, May 26, 2009 3:55 PM To: pymol-users@lists.sourceforge.net Cc: Chaix Denis; support; pymol-users@lists.sourceforge.net Subject: [PyMOL] surface of ligand Dear users How can I obtain the surface of a ligand in protein pdb file. I just need the simple surface, i doesn't need in this case, the electrostatic surface. Thanks -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___ 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] FYI: Mid-range stereo 3D projector / emitter / glasses bundle
Stereo-3D-enthusiasts, Ad include below, just FYI -- no affiliation with DeLano Scientific -- though we have used products from these companies and found them effective. It appears that you can now set up a small conference room for active-stereo 3D visualization with glasses for 4 people for a mere $7,500 USD. I suspect you could get another half dozen glasses for a total cost under $10k (not including a stereo-3D capable PC of course). For small groups in small or mobile settings, this bundle might make more sense than the high-end Christie Mirage / Z-Screen / polarized glasses solution. Cheers, Warren -- LIGHTSPEED DESIGN AND RealD PRO INTRODUCE 3D BUNDLE Offer Includes DepthQ HD 3D Projector, CrystalEyes 3 Eyewear and EXXR Emitter BELLEVUE, WA - May 20, 2009: Lightspeed Design, Inc., a developer of 3D stereoscopic projectors, and RealD PRO, a division of leading 3D technology and visualization equipment provider, RealD, are pleased to announce the release of the NEW DepthQ(r)/RealD PRO Bundle. The DepthQ(r)/RealD PRO Bundle consists of a DepthQ(r) HD 3D projector, four CrystalEyes(r) 3 professional liquid crystal shutter eyewear, and an EXXR long range wide-angle IR Theatre Emitter for a total price of $7500. In addition, customers purchasing a DepthQ(r)/RealD PRO Bundle from Lightspeed will be able to purchase additional CrystalEyes(r) 3 eyewear under special pricing. Chris Ward, President of Lightspeed Design, Inc. said Combining these state-of-the-art stereoscopic products into one package brings added value to our professional customers who need high quality, stereoscopic HD 3D technology. DepthQ(r) HD 3D Projectors offer rock-solid, 120Hz stereo 3D at 1280x720 resolution. These bright, professional-level 3D projectors can easily display 9 ft (2.7m) wide 3D high-definition images using the latest Texas Instruments DLP(r) and BrilliantColor(tm) technologies for stunning colors and a 2000:1 contrast ratio. CrystalEyes(r)3 is the industry standard for engineers and scientists who develop, view and manipulate 3D computer graphics models in CAVEs, theaters and immersive environments. CrystalEyes(r) 3 is the leader for 3D visualization in molecular modeling, virtual prototyping, and aerial photography/mapping. The EXXR Long Range Theatre Emitter offers a 130 degree infrared spread transmitting up to 70ft (21m) making it the most powerful active eyewear synchronization emitter in the world. To order now and take advantage of this special bundle pricing, please contact Lightspeed at http://www.depthq.com/contact.html or call our sales department at +1-425-637-2818. Subscribe in a reader to DepthQ Latest News About Lightspeed Design, Inc. Lightspeed is one of the world's premiere designers of stereoscopic 3D presentations and software technologies, with considerable technical expertise in projection, optics and electronics. Clients include Pfizer, Intuitive Surgical, Microsoft, Harvard Munich Universities, US Army, NASA, JPL, DreamWorks SKG, IMAX, and Walt Disney Animation. Lightspeed's headquarters is in Bellevue, Washington, USA. For more information, visit us at http://www.lightspeeddesign.com or contact the company directly at sa...@lightspeeddesign.com or +1-425-637-2818. About RealD PRO RealD PRO is the professional division of RealD, a leading 3D technology developer and supplier of 3D visualization equipment solutions including 3D-enabling eyewear, infrared eyewear synchronization devices, 3D-ready DLP(r) TV kits, industrial projectors, monitor peripherals, passive 3D solutions and 3D format converters. RealD PRO is a one-stop source for 3D information, equipment and technical support, enabling 3D for everything from virtual prototyping to entertainment content creation. http://www.reald.com Press contact: Chris Ward Lightspeed Design, Inc. +1-425-637-2818 DepthQ(r) is a registered trademark of Lightspeed Design, Inc. CrystalEyes(r) is a registered trademark of RealD. Digital Light Processing, DLP(r) and BrilliantColor(tm) are registered trademarks of Texas Instruments. All rights reserved. -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] When in doubt, go with nVidia.
Folks, For quite some time now, we have ourselves experienced and continued to receive complaints regarding graphics artifacts and other glitches with ATI/AMD Radeon HD graphics chips on multiple platforms. Though we haven't had time to investigate everything to our satisfaction, it is worth noting that such issues are conspicuously absent from those using recent nVidia and Intel graphics chips, and that they also do not occur with older ATI chips -- only the newer HD -branded models. Therefore, if you are given a choice with a new purchase today, we strongly recommend going with nVidia-based graphics chips for running PyMOL. Intel chips work fine too though they aren't typically as fast. Just to be clear, we don't know for certain yet whether the fault lies with PyMOL, with the OpenGL drivers, or with the ATI graphics chips themselves. but if you simply buy nVidia, then you can entirely avoid having to deal with AMD/ATI-specific OpenGL problems. Eventually these problems will likely be worked out - the chips are just glitchy, not DOA - but there is a lot to be said for deliberately avoiding problematic scenarios altogether. Cheers, Warren -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Documentation and advice for external GUI Movies commands?
Jean, Assuming that you are using the most recent PyMOL 1.2 beta build, first create a Scene for each display you wish to show. (To do that, show everything the way you want and then select Append from the Scene menu. Repeat the process for each view / color / representation you wish to show. You can PgUp / PgDown through defined Scenes.) Then, to create the movie, select Program - Scene Loop - Y-Rock - # seconds each from the Movie menu. Now you can write out the movie as either a series of PNG files or an MPEG file using Save Movie As... from the File menu. Using scenes to create movies is a lot easier than messing around with scripts : )! Cheers, Warren From: Jasinski, Jean Marie [mailto:jean.jasin...@ucdenver.edu] Sent: Tuesday, May 19, 2009 11:06 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Documentation and advice for external GUI Movies commands? My goal is to make a simple movie from PyMol for inclusion in a powerpoint presentation. I understand how to use the png files to make an avi file. What I need help with is using the external GUI Movie commands to make my movie. I want to use the x-rock command, turn on my ligand, x-rock again, turn off ligand, display second ligand and repeat the process. So far, I've only used the external GUI command line to do util.mrock. I can't find documentation for the Movie commands (Program, Update Program, etc.). I figure I could use a script to do all the actions I need, but I can't figure out how to call Movie/Program/Static Loop/X-rock,. Thanks, Jean Jasinski, Ph.D. -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] vacuum electrostatics
Denis, Sorry, PyMOL only has protein charges coded at present. Perhaps the APBS project's pdb2pqr utility might be able to assign charges to canonoical ligands (such as ATP)? http://apbs.sourceforge.net Cheers, Warren -Original Message- From: Chaix Denis [mailto:denis.ch...@cbs.cnrs.fr] Sent: Monday, May 18, 2009 9:10 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] vacuum electrostatics Dear users I'm trying to compare the electrostatic charge surface of my protein with and without ligand, by using the command generate vacuum electrostatics. that's works fine for the protein without ATP but that doesn't work with the ligand.The surface obtaine doesn't take account the ligand thanks -- CHAIX Denis Centre de Biochimie Structurale INSERM U554/CNRS 5048 29 rue de Navacelles F-34090 Montpellier, France Tel: 33 4 67 41 77 21 Fax: 33 4 67 41 79 13 e-mail:denis.ch...@cbs.cnrs.fr http://www.cbs.cnrs.fr -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] create double bonds in small molecules
Tom, set valence edit_mode Ctrl-right-click on the bond Ctrl-W seems to do the trick. Perhaps there's a problem with the version of PyMOL you're using? Cheers, Warren From: Thomas S. Leyh, Ph. D. [mailto:l...@aecom.yu.edu] Sent: Thursday, May 14, 2009 10:13 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] create double bonds in small molecules Hi, I've been trying to get PyMOL to display a double bond at the position of the vinyl in the attached, small-moleculePDB for some time. The PDB was generated by converting a smiles representation of isopentenly diphosphate (obtained from PubChem) using Corina. The number of attached atoms at the vinyl group is correct, but PyMOL doesn't display the double bond. Cycling the bond valence produces a single-bond version (with added protons), but stops there - it won't cycle through triple, double, single. Downloaded a PDB of fumarate that does display double bonds in response to Set Valence - so, my version of PyMOL (1.1beta2, Vista environment) seems fine. Thoughts? Thanks, Tom -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Error: unknown type
Shiven, It appears the script was flawed: names = cmd.get_names(sel1) should be: names = cmd.get_names(selection=sel1) I've updated it on the Wiki. Cheers, Warren -Original Message- From: Shiven Shandilya [mailto:shiven.shandi...@gmail.com] Sent: Monday, May 11, 2009 4:47 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Error: unknown type Hello List, Any ideas on why this script keeps failing in the newer PyMOL builds... http://pymolwiki.org/index.php/Zero_residues I keep getting the error message: Error: unknown type: '1hpv' where 1hpv is an actual pdb file/object I am running pymol 1.2b5 rev. 3706 (compiled from svn) on Ubuntu 8.10 Anyone else face a similar issue, or is it just me Thanks! --Shiven -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Vacuum electrostatics
Mark, Should be fixed now (in rev 3720). Cheers, Wawrren -Original Message- From: Mark Wehner [mailto:mark.weh...@rub.de] Sent: Monday, May 11, 2009 12:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Vacuum electrostatics Hi everyone, in the newer version of pymol I realized it is not possible to generate vacuum electrostatics, there's an error while assigning the formal charges. The error message is: Alter-Error: Aborting on error. Assignment may be incomplete. File string, line 1 formal_charge=0;flags=flags0x-8388609 I build the source code (rev 3719) using Python 2.6.2. Is anyone experiencing similar problems at the moment? Mark -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Non-planar clipping?
David, This is a weak area for PyMOL. One thing to try is to switch to an animation with multi-layered transparency, two_sided lighting (and other tweaks) to help show the entire binding site volume. The approach isn't perfect, but it may help: fetch 1gzm, async=0 remove not a// select my_ligand, a/ret/, enable=0 hide show st, my_ligand set transparency, 0.85 set transparency_mode, 1 ;# multi-layer set two_sided_lighting set ray_transparency_contrast, 3 ;# layer-dependent set ray_transparency_oblique, 1.5 ;# normal-dependent select carve_sele, my_ligand, enable=0 set surface_carve_selection, carve_sele set surface_carve_cutoff, 4.5 set surface_quality, 1 show surface, my_ligand expand 6 zoom vis set ray_trace_frames set cache_frames bg white mset 1 x30 orient my_ligand zoom my_ligand, 3 movie.rock mplay # now wait a few minutes for the movie to render and play Cheers, Warren From: Margulies, David (NIH/NIAID) [E] [mailto:dmargul...@niaid.nih.gov] Sent: Thu 5/7/2009 4:07 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Non-planar clipping? Hi, I would like to make a clipped illustration of a peptide-ligand binding site, a sliced-image as it were, but because the binding site consists of several non-linear pockets, I can't visualize all in the same clipping view. Is there a way to make a non-planar section? Or a straightforward way of superposing several different clipping planes with a different level of transparency to visualize all pockets with the superposed peptide-ligand? -- David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immunology, NIAID, NIH Bldg. 10; Room 11N311 10 Center Drive Bethesda, MD 20892-1892 email: d...@nih.gov phone: 301-496-6429 fax: 301-496-0222 ___ The information in this e-mail and any of its attachments are confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender¹s own and not expressly made on behalf of the NIAID by one of its representatives. -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Vector-Based Figure Export
Sean, We don't have vector export, but PyMOL can generate a high-resolution BW transparent-background raster image as illustrated below: load $PYMOL_PATH/test/dat/1tii.pdb as cartoon set ray_trace_mode, 2 set ray_trace_gain, 1 unset antialias unset opaque_background unset depth_cue bg white ray 3600 That's enough pixels to fill a 8.5x11 page at over 300 dpi... Cheers, Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Fri 5/1/2009 6:22 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Vector-Based Figure Export Hi Warren, I know that there has been some discussion on implementing a vector-based figure export. I was wondering if there were any updates on this? I think that this would be an amazing feature to have. Thanks! Sean Internet Explorer 8 makes surfing easier. Get it now! http://go.microsoft.com/?linkid=9655264 From: Sean Law [mailto:magic...@hotmail.com] Sent: Fri 5/1/2009 6:22 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Vector-Based Figure Export Hi Warren, I know that there has been some discussion on implementing a vector-based figure export. I was wondering if there were any updates on this? I think that this would be an amazing feature to have. Thanks! Sean Internet Explorer 8 makes surfing easier. Get it now! http://go.microsoft.com/?linkid=9655264 -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Grid_mode - reference structure
Martin, set grid_slot, -2, object-name for the object you wish to spread across all grid slots. Cheers, Warren -Original Message- From: Höfling Martin [mailto:martin.hoefl...@gmx.de] Sent: Tue 5/5/2009 5:02 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Grid_mode - reference structure Hey Folks, First of all: Grid Mode is awesome! Maybe I have overlooked a feature, but it seems to me that it is impossible to show a reference structure in all grids. Is there a better way than duplicating the object for every grid cell? Best Martin -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] diehedral angle
Vivek, # new command in 1.2b5 - fabricate peptide, ALA trimer: fab AAA # set a dihedral value ro 180 degrees. set_dihedral 1/C, 2/N, 2/CA, 2/C, 180 Cheers, Warren From: Vivek Ranjan [mailto:vran...@gmail.com] Sent: Tue 5/5/2009 12:09 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] diehedral angle Hello, I would like to change some of the diehedral angles in a polymer systems. I know how to measure diehedral angle. However, I don't know how to change it ? Any advice is greatly appreciated. -- Thank you and Regards, Vivek Ranjan -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users