Re: [PyMOL] alignment of metal coordination
From: ccp4...@hotmail.com To: pymol-users@lists.sourceforge.net Date: Fri, 8 Nov 2013 19:53:50 -0600 Subject: [PyMOL] alignment of metal coordination Hi, Is it possible to align two structure based on metal coordination or metal-coordinating residues? What is good way to do it? Is this a 1-D alignment or spatial ? There are conserved sequence DB's and of course if you want to check there are things like citeseer and pubmed as well as google scholar for finding algorithms if nothing exists in pymol. Maybe someone can comment on how to do this in pymol but you can always define your own figure of merit and optimize that as a function of relative orientation. I suppose you can define an ordering of residues based on interactions with metals. I actually downloaded several orderings from ( hotmail makes it almost impossible any more to insert links into plain text messages now thinking I must mean html ) http://www.expasy.org/tools/protscale.html\ for exampl,e, Hphob.Argos.tr KDRENQPHYSWTGCAVMILF I appreciate your guidance. Thanks SDY -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ 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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ 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] Electrostatic potential surface
I have a similar requirement, taking density and potential dstriutbutions from jdftx which are written as plain binarry doubles. I use a script and some code to create an xplor file which seems to work but I have to adjust the position and scale to let it overlay the ion positions that I read from an xyz file. AFAICT xplor is about the only easy format that pymol takes but I was debating about trying to find others. i think I dug through my older version of pymol, went to the effort of changing it all to c++/extern c and then dropped it. The xplor approch seems to work well enough for now. Is there an easier way? Thanks. Date: Wed, 27 Mar 2013 13:41:24 +0400 From: jmsstarli...@gmail.com To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electrostatic potential surface Dear PyMol users! I wounder to know about built-in PyMol option for electrostatic potential visualisation. For example I have pdb coordinates of my protein as well as its electrostatic potential distribution (calculated by another software). Using MolMol with both of that files I can visualize the electrostatic potential surface by means of PaintSurface option. Can I do the same with the PyMOl? Thanks for help, James -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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 -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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 to 3D PDF
From: blaine-moo...@ouhsc.edu To: tlin...@gmail.com Date: Wed, 13 Mar 2013 04:45:59 -0500 CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL to 3D PDF PyMOL will also save surfaces in addition to cartoons to vwrl and idtf. Any representation composed of triangular surfaces should work. Thus, PuMOL fails to save labels to vmrl or idtf. This is another major advantage of JMOL over PyMOL at present. When you make 3D PDF how well do they display and manipulate? I thought this would be a nice feature for even 3D plots and IIRC tried it with an example from CRAN's R a while back , I can't remember how it came out in detail but seem to recall the pages took a while to load etc and at the time it was easier to load the data in an app rather than try to publish it that way. for many actual pubs, they provide links in supplementary information section and it may be just as easy to publish a viewer script along with static images for illustration. A plugin would be nice, I always liked CHIME and that worked well on Internet Explorer about 10 years ago. Blaine Mooers Assistant Professor Director Macromolecular Crystallography Lab Member Stephenson Cancer Center Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-moo...@ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d- X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory SAXS Links webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0 From: Troels Emtekær Linnet [tlin...@gmail.com] Sent: Wednesday, March 13, 2013 4:19 AM To: Mooers, Blaine H.M. (HSC) Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL to 3D PDF Yeah. That is a cool feature, and is kind of the future of publishing. :-) Or at least, a very powerful tool for teaching. But it is sad that it only have cartoon export. I wish that it could include other representations. For now I use Jmol, which can export the whole representation in the window. I can import small molecules through. Files-Get MOL- And then CAS number or smiles. For proteins I scoop into rcsb.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091, and find the protein in the Jmol online viewer. (Just changing to white back ground). Right click in Jmol window-Export file-Export IDTF 3D model. That saves a .idtf file, and a .tex file ready for LaTeX. Rename the .idtf file, so it only ends on .idtf and not: filename.xyz.idtf Simpy converting the .idtf to .u3d as instructed in, http://www.pymolwiki.org/index.php/3d_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=25a32bf64cd6f0227c7a8a73361f42721f9a6a377010deef4b50acdb49f29ccd) and you are ready to go from the given .tex file. (Removing the last looong comment section.) With a little practice, it only takes 3 min, to have 3d implementation of your molecule in teaching material / beamer presentation. I wish that could be implemented in PyMOL, and I have been looking for a wish list, but I don't know where that exists? Best Troels Emtekær Linnet Ved kløvermarken 9, 1.thhttps://urldefense.proofpoint.com/v1/url?u=http://1.thk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=5edb01bafbd605fcdadfe489b90dfe0d526e9a96b0ba86b04791e8d92bc46a63 2300 København S Mobil: +45 60210234 2013/3/12 Mooers, Blaine H.M. (HSC) blaine-moo...@ouhsc.edumailto:blaine-moo...@ouhsc.edu I saw Jason Vertrees update of http://www.pymolwiki.org/index.php/3d_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=25a32bf64cd6f0227c7a8a73361f42721f9a6a377010deef4b50acdb49f29ccd. It has the address to the source code for u3d-1.4.3. I could not compile earlier versions of this program on a Mac running Snow
Re: [PyMOL] PyMOL to 3D PDF
I hit this link, the image was blank in evince but did come up in Adobe Reader 9 if I click on it ( also prompted for security issues) http://www.fys.ku.dk/~tlinnet/1zqa.pdf It was a bit sluggish but did zoom and rotate acceptably. I guess in this case the more useful thing would be all the information needed to manipulate in the dedicated app, in this case pymol, but it seems the pdf would be helpful for those without it. My concern is that in the past it had not been functional and only served to obscure data that the author intended to be useful to others. It is getting better however :) I may try this again if I have 3D data from pymol or R Thanks. From: tlin...@gmail.com Date: Wed, 13 Mar 2013 13:01:17 +0100 Subject: Re: [PyMOL] PyMOL to 3D PDF To: marchy...@hotmail.com CC: pymol-users@lists.sourceforge.net Hi Mike. Try the example pdfs at: http://pymolwiki.org/index.php/3d_pdf 1zqa PDFhttp://www.fys.ku.dk/~tlinnet/1zqa.pdf beamer 1zqa PDFhttp://www.fys.ku.dk/~tlinnet/beamer_1zqa.pdf Troels Emtekær Linnet Ved kløvermarken 9, 1.thhttp://1.th 2300 København S Mobil: +45 60210234 2013/3/13 Mike Marchywka marchy...@hotmail.commailto:marchy...@hotmail.com From: blaine-moo...@ouhsc.edumailto:blaine-moo...@ouhsc.edu To: tlin...@gmail.commailto:tlin...@gmail.com Date: Wed, 13 Mar 2013 04:45:59 -0500 CC: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL to 3D PDF PyMOL will also save surfaces in addition to cartoons to vwrl and idtf. Any representation composed of triangular surfaces should work. Thus, PuMOL fails to save labels to vmrl or idtf. This is another major advantage of JMOL over PyMOL at present. When you make 3D PDF how well do they display and manipulate? I thought this would be a nice feature for even 3D plots and IIRC tried it with an example from CRAN's R a while back , I can't remember how it came out in detail but seem to recall the pages took a while to load etc and at the time it was easier to load the data in an app rather than try to publish it that way. for many actual pubs, they provide links in supplementary information section and it may be just as easy to publish a viewer script along with static images for illustration. A plugin would be nice, I always liked CHIME and that worked well on Internet Explorer about 10 years ago. Blaine Mooers Assistant Professor Director Macromolecular Crystallography Lab Member Stephenson Cancer Center Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-moo...@ouhsc.edumailto:blaine-moo...@ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d- X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory SAXS Links webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0 From: Troels Emtekær Linnet [tlin...@gmail.commailto:tlin...@gmail.com] Sent: Wednesday, March 13, 2013 4:19 AM To: Mooers, Blaine H.M. (HSC) Cc: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL to 3D PDF Yeah. That is a cool feature, and is kind of the future of publishing. :-) Or at least, a very powerful tool for teaching. But it is sad that it only have cartoon export. I wish that it could include other representations. For now I use Jmol, which can export the whole representation in the window. I can import small molecules through. Files-Get MOL- And then CAS number or smiles. For proteins I scoop into rcsb.orghttp://rcsb.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091https://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0am=9qhiQpTD7yw1v1CYn82swYWLHkc/kmViU2tMT7DUu9c%3D%0as=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091, and find the protein in the Jmol online viewer. (Just changing to white back ground). Right
Re: [PyMOL] Building of the Carbon lattice
Where do you get the x_shift and y_shift values? I ended up writing a program to take bond lengths and directions relative to select coord systems to generate periodic or almost periodic things. Right now polyenes but extensible. Is there some program that does this easily? This allows me to write a simple TcL script and reorient the whole molecule by changing one parameter . I don't currently have a way to include library items, like say a methyl group, and I was debating about doing this in python but I wanted to have easy access to lapack etc for later extensions. Thanks. Date: Fri, 4 Jan 2013 11:13:39 +0100 From: spel...@users.sourceforge.net To: jmsstarli...@gmail.com CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Building of the Carbon lattice Hi James, just calculate the coordinates and write them out in PDB format, quite simple task. Try the attached script. Cheers, Thomas James Starlight wrote, On 01/04/13 09:14: Hi Mike, Chimera can build such lattices by means of it's build structure module. On other hand I want to build such 2D lattices http://imageshack.us/photo/my-images/543/lattice.png/ made from SP3 carbons as the nodes via some automatic script to obtain lattices with desired dimensions. James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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 -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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] Building of the Carbon lattice
well, my point was just that they seem to be orientation sensitive although I didn't look at entire script in any detail and that if you wanted to re-orient the fragment you would have to recalculate these. Nothing difficult but just easier if there was a script that said something like put this thing here with this orientation wrt some prior fragment ( no absolute directions at this point. ) Date: Fri, 4 Jan 2013 15:52:13 +0100 From: spel...@users.sourceforge.net To: marchy...@hotmail.com CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Building of the Carbon lattice Hi Mike, I simply measured x_shift and y_shift from a cyclohexane fragment. Use the graphical Builder or the fragment command to load stuff from the fragment library. PyMOL fragment cyclohexane Cheers, Thomas Mike Marchywka wrote, On 01/04/13 15:44: Where do you get the x_shift and y_shift values? I ended up writing a program to take bond lengths and directions relative to select coord systems to generate periodic or almost periodic things. Right now polyenes but extensible. Is there some program that does this easily? This allows me to write a simple TcL script and reorient the whole molecule by changing one parameter . I don't currently have a way to include library items, like say a methyl group, and I was debating about doing this in python but I wanted to have easy access to lapack etc for later extensions. Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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] which code actually executes to load axplor file? Debugstatements not executing.
Thanks but it looks like I am ok now ( aside from orignally posting this on the wrong list LOL). My python build still hangs and has problems with the list area on right but the configure/make build process works fine and I could find the problem. Generally error checking is the last thing ayone wants to do and the positions sensitive fields are a big problem to find from a segfault. I think this is the 5..0.2 open source version. In any case, I wanted to allow for input of some custom file formats and maybe integrate with some of my old code and it now looks like I can do that. Would be happy to contribute at some point if I get something that works LOL. Thanks. Date: Thu, 3 Jan 2013 12:32:01 +0100 From: thomas.hol...@schrodinger.com To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing. Hi Mike, I guess you are on Linux with Open-Source PyMOL, right? Can you send me the xplor file that causes PyMOL to segfault? From your backtrace it looks like the problem is related to crystal symmetry information. If you want to load some format which is not yet supported by PyMOL, the easiest solution is to convert it to some already supported format on the fly and feed that to PyMOL, if possible. Cheers, Thomas Mike Marchywka wrote, On 01/02/13 17:01: I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for xplor is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering (I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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] which code actually executes to load axplor file? Debugstatements not executing.
never mind, it looks like the name case changes and opening in GDB gave me a bt, fwiw, presumably I can figure this out now... PyMOLcmd.load_raw(content, 'xplor', 'map',quiet=0) ObjectMapLoadXPLOR: Loading... Program received signal SIGSEGV, Segmentation fault. transform33f3f (m1=0xffc0ffc00044, m2=0x7fffa070, m3=0x7fffa080) at Vector.c:677 677 m3[0] = m1[0] * m2r0 + m1[1] * m2r1 + m1[2] * m2r2; (gdb) bt #0 transform33f3f (m1=0xffc0ffc00044, m2=0x7fffa070, m3=0x7fffa080) at Vector.c:677 #1 0x75761fdd in ObjectMapXPLORStrToMap (I=0x1dbf320, XPLORStr=optimized out, state=optimized out, quiet=0) at ObjectMap.c:3204 #2 0x7576b838 in ObjectMapReadXPLORStr (quiet=0, state=-1, XPLORStr=0x7fffeb685034 \n 4 !NTITLE\n line 2 desc\n line 3 desc\n line 4 desc\n line 5 desc\n 080 0 080 160 0 160 080 0 080 \n 0.85336E+02 0.85336E+02 0.75650E+02 0.9E+02 0.9E..., I=0x1dbf320, G=0xeb1300) at ObjectMap.c:4474 #3 ObjectMapLoadXPLOR (G=0xeb1300, obj=0x0, fname=optimized out, state=-1, is_file=0, quiet=0) at ObjectMap.c:5541 #4 0x7582c712 in ExecutiveLoad (G=0xeb1300, origObj=0x0, content=0x7fffeb685034 \n 4 !NTITLE\n line 2 desc\n line 3 desc\n line 4 desc\n line 5 desc\n 080 0 080 160 0 160 080 0 080 \n 0.85336E+02 0.85336E+02 0.75650E+02 0.9E+02 0.9E..., content_length=optimized out, content_format=26, object_name=0x7fffb210 map, state=-1, zoom=-1, discrete=0, finish=1, multiplex=-1, quiet=0, plugin=0x0) at Executive.c:3724 #5 0x7586a572 in CmdLoad (self=0x76177dc8, args=optimized out) at Cmd.c:7866 #6 0x004b66b9 in PyEval_EvalFrameEx () #7 0x004bcdbd in PyEval_EvalCodeEx () ---Type return to continue, or q return to quit--- #8 0x004b6c34 in PyEval_EvalFrameEx () #9 0x004bcdbd in PyEval_EvalCodeEx () #10 0x004bd892 in PyEval_EvalCode () #11 0x004dcd82 in ?? () #12 0x004dd7a5 in PyRun_StringFlags () #13 0x004bafc6 in PyEval_EvalFrameEx () #14 0x004bcdbd in PyEval_EvalCodeEx () #15 0x004b6c34 in PyEval_EvalFrameEx () #16 0x004bcdbd in PyEval_EvalCodeEx () #17 0x004b6c34 in PyEval_EvalFrameEx () #18 0x004bcdbd in PyEval_EvalCodeEx () #19 0x0044914f in ?? () #20 0x0042423c in ?? () #21 0x0042704d in PyObject_CallFunction () #22 0x756f7414 in PFlushFast (G=0xeb1300) at P.c:2665 #23 0x7586b616 in CmdFlushNow (self=0x76177dc8, args=optimized out) at Cmd.c:2931 #24 0x004b66b9 in PyEval_EvalFrameEx () #25 0x004bcdbd in PyEval_EvalCodeEx () #26 0x004b6c34 in PyEval_EvalFrameEx () #27 0x004bcdbd in PyEval_EvalCodeEx () #28 0x004b6c34 in PyEval_EvalFrameEx () #29 0x004bcdbd in PyEval_EvalCodeEx () ---Type return to continue, or q return to quit--- #30 0x0044914f in ?? () #31 0x0042423c in ?? () #32 0x004242e7 in ?? () #33 0x00427248 in PyObject_CallMethod () #34 0x7586fd96 in MainDrawLocked () at main.c:811 #35 0x7586ff53 in MainDraw () at main.c:1081 #36 0x747a0220 in ?? () from /usr/lib/libglut.so.3 #37 0x747a3939 in fgEnumWindows () from /usr/lib/libglut.so.3 #38 0x747a065a in glutMainLoopEvent () from /usr/lib/libglut.so.3 #39 0x747a0f65 in glutMainLoop () from /usr/lib/libglut.so.3 #40 0x75871504 in launch (options=0xeaf520, own_the_options=optimized out) at main.c:1955 #41 was_main () at main.c:2006 #42 0x75853dd4 in CmdRunPyMOL (self=0x76177df0, args=optimized out) at Cmd.c:4771 #43 0x004b66b9 in PyEval_EvalFrameEx () note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency From: marchy...@hotmail.com To: pymol-users@lists.sourceforge.net Date: Wed, 2 Jan 2013 11:01:52 -0500 Subject: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing. I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for xplor is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering ( I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much
Re: [PyMOL] Building of the Carbon lattice
What does Chimera do? I finally wrote my own c++ tool that let's a TcL script specify a molecule's layout in terms of relevance like bond length and angle. I decided it was worth the effort since I didn't want to look around much for existing stuff and would eventually add my own stuff for analysis. The real decision was to learn python or just use TcL. I guess if I was looking for a tool to generate from a script I'd probably prefer python. Thanks. Date: Fri, 28 Dec 2012 05:42:27 -0800 From: jmsstarli...@gmail.com To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Building of the Carbon lattice Hi Tsjerk! This is the example of such lattice which I've built using Chimera! http://imageshack.us/photo/my-images/543/lattice.png/ this is simple model of the Carbon-contained lattice without hydrogens. So I'd like to build such lattices from different atoms as nodes defining only atom type as well as number of nodes. Also I'd like to simulate this model using PBC so it seems that big dimensions of such lattice doesn't matter, doesn’t it ? ( It will be simpler to build smaller symmetric model ) James -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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 -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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 with alignments/ more general create and align question
I don't want to hijack the thread but I was curious if you can point to few pymol features for generating and rotating molecules and how they would play with other tools. For example, if I just go download pdb files or take output from DFT, it may be easier to do analysis with certain alignments. Similarly, I want to generate hypothetical molecules for various tests and wanted some easy way to do that. There are many graph, shape, or geometry tools available in various fields, maps, CAD etc and apparently they are tools for drawing or editing molecules. However, I was just looking for something that works from command line and is reasonably easy to integrate with other things. Apparently pymol is all based on python and presumably features, like the plugins you pointed me to earlier, are easy to mix and match with other tools but not sure offhand how to approach this. Right now, I'm making my own c++ tool using Tcl front end so that I can eventually use all the math libraries like lapack and boost as I want to do larger molecules( and use these for various types of alignments that could generate large matricies ). Should I use python or just use something that pymol already has? The immediate need is just to generate xyz files that look like short polyenes and be able to perturb them using a script. So for this I end up with Tcl input that looks like a list of atom and direction commands but there is probably some way to do this much with existing tools. Thanks. From: jason.vertr...@schrodinger.com Date: Tue, 11 Dec 2012 07:38:32 -0600 To: jonat...@strubi.ox.ac.uk CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Help with alignments Hi Jon, align prot1 and chain A, prot2 and chain X 'super' and 'cealign' should work similarly. Cheers, -- Jason On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes jonat...@strubi.ox.ac.uk wrote: I am wanting to align proteins based on superposition of particular chains. Is it possible to do the superposition based on the chains, but to move, in this case the entire complex ??? Thanks Jon Sent from my iPad -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
From: jason.vertr...@schrodinger.com Date: Mon, 26 Nov 2012 10:37:52 -0600 Subject: Re: was: [PyMOL] Mobile PyMOL Problem and Solution/ Now: pdb or related libraries To: marchy...@hotmail.com CC: pymol-users@lists.sourceforge.net Hi Mike, I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. We have an API for accessing structures remotely. For example, load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb, myMolecule You could easily create a PyMOL plugin (http://www.pymolwiki.org/index.php/Plugins_Tutorial) that takes advantage of this site very simply using the load command and formatted URLs. Thanks, I didn't know it would be that simple and that looks like a good way to learn python. Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case, what pymol facilities are there for adding them? Apparently you have some editing capabilites and analyses, I thought there may be some way to guess approximately where the hydrogens should go and then export the new file. This is probably obvious from a quick google search on basic capabilites but it also sounds as if there may be less well known specialized tools for doing less common things like this. I hope your meal was tasty. how can you enjoy it without the pdb file on the screen and optimizing in DFT? LOL. Cheers, Thanks. -- Jason From: jason.vertr...@schrodinger.com Date: Fri, 2 Nov 2012 18:57:38 -0500 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mobile PyMOL Problem and Solution Greetings, On Oct 28th, the folks at the PDB made some changes to their PDB Web Services interface. This change broke Mobile PyMOL's ability to search for and download PDBs. I haven't bothered to look at this specific situation but this a problem with many sites and automated interaction. NCBI has a nice eutils interface that has remained stable for a while, I'd been trying to get more groups to offer a web interface designed for automated interactions. FWIW, http://www.ncbi.nlm.nih.gov/books/NBK25500/ Do you have automated access to this library for example, http://www.ncbi.nlm.nih.gov/Structure/index.shtml they also have their own viwer, for example, http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml but pymol seems a bit more extensive. I have updated Mobile PyMOL and will soon resubmit it to the AppStore for verification and release. This process takes typically takes no less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users please use the following technique to acquire structures: (1) Using Safari on the iPad browse to the www.pdb.org and find the structure you want. (2) Click Download Files from the upper right hand side of the structure's page and then select PDB File (Text). (3) Click Open in PyMOL. Happily, as a long-term solution, I've established contact with the PDB Web Services Group and we'll now be made aware of future changes. The PDB is an extremely valuable resource in the community and I'm glad we could work this out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d ___ 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers,
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
From: jason.vertr...@schrodinger.com Date: Tue, 27 Nov 2012 12:37:41 -0600 Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries To: marchy...@hotmail.com CC: pymol-users@lists.sourceforge.net Mike, Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case, what pymol facilities are there for adding them? Apparently you have some editing h_add object_name Type, help h_add or check out h_add on the PyMOLWiki (http://www.pymolwiki.org/index.php/H_Add). Thanks, applying to the pdb I had seems to have worked but it didn't think much of the double bonds and added extra's but presumably I can delete and rotate more easily than adding all them manually. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Keep yourself connected to Go Parallel: DESIGN Expert tips on starting your parallel project right. http://goparallel.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
[PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. From: marchy...@hotmail.com To: jason.vertr...@schrodinger.com; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Mobile PyMOL Problem and Solution Date: Fri, 2 Nov 2012 20:43:41 -0400 From: jason.vertr...@schrodinger.com Date: Fri, 2 Nov 2012 18:57:38 -0500 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mobile PyMOL Problem and Solution Greetings, On Oct 28th, the folks at the PDB made some changes to their PDB Web Services interface. This change broke Mobile PyMOL's ability to search for and download PDBs. I haven't bothered to look at this specific situation but this a problem with many sites and automated interaction. NCBI has a nice eutils interface that has remained stable for a while, I'd been trying to get more groups to offer a web interface designed for automated interactions. FWIW, http://www.ncbi.nlm.nih.gov/books/NBK25500/ Do you have automated access to this library for example, http://www.ncbi.nlm.nih.gov/Structure/index.shtml they also have their own viwer, for example, http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml but pymol seems a bit more extensive. I have updated Mobile PyMOL and will soon resubmit it to the AppStore for verification and release. This process takes typically takes no less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users please use the following technique to acquire structures: (1) Using Safari on the iPad browse to the www.pdb.org and find the structure you want. (2) Click Download Files from the upper right hand side of the structure's page and then select PDB File (Text). (3) Click Open in PyMOL. Happily, as a long-term solution, I've established contact with the PDB Web Services Group and we'll now be made aware of future changes. The PDB is an extremely valuable resource in the community and I'm glad we could work this out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d ___ 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 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
Date: Sun, 25 Nov 2012 23:49:26 +0100 From: spel...@users.sourceforge.net To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries Hi Mike, you can fetch molecular files from any web address with the load command. Examples: File type recognized from file extension: PyMOL load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb Thanks, it sounded like the original poster was refering to a larger facility to find pdb files in a variety of libraries. If I know where the file is I can usually get it with wget but if tere is some search API or facility that may be helpful. I am finding some pdb collections online but thought they may be listed somewhere. In any case, I eventually realized that the pdb does not have the hydrogens and I can't find one that may. Would it be reasonable to try to use pymol to add them? I only need artists conception as presumably the DFT optimization will make it more accurate. File type given with format argument: PyMOL load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443disopt=3DSaveSDF, format=sdf Also, Mobile PyMOL (for the iPad) has it's own server capabilities, including support for PubChem, PDB, Dropbox, etc. Cheers, Thomas Mike Marchywka wrote, On 11/25/12 17:26: I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
fwiw, I did find mol2 format at this location which is just fine for my scripts, http://zinc.docking.org/substance/1633229 Thanks. From: marchy...@hotmail.com To: spel...@users.sourceforge.net; pymol-users@lists.sourceforge.net Date: Sun, 25 Nov 2012 19:00:08 -0500 Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries Date: Sun, 25 Nov 2012 23:49:26 +0100 From: spel...@users.sourceforge.net To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries Hi Mike, you can fetch molecular files from any web address with the load command. Examples: File type recognized from file extension: PyMOL load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb Thanks, it sounded like the original poster was refering to a larger facility to find pdb files in a variety of libraries. If I know where the file is I can usually get it with wget but if tere is some search API or facility that may be helpful. I am finding some pdb collections online but thought they may be listed somewhere. In any case, I eventually realized that the pdb does not have the hydrogens and I can't find one that may. Would it be reasonable to try to use pymol to add them? I only need artists conception as presumably the DFT optimization will make it more accurate. File type given with format argument: PyMOL load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443disopt=3DSaveSDF, format=sdf Also, Mobile PyMOL (for the iPad) has it's own server capabilities, including support for PubChem, PDB, Dropbox, etc. Cheers, Thomas Mike Marchywka wrote, On 11/25/12 17:26: I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] Mobile PyMOL Problem and Solution
From: jason.vertr...@schrodinger.com Date: Fri, 2 Nov 2012 18:57:38 -0500 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mobile PyMOL Problem and Solution Greetings, On Oct 28th, the folks at the PDB made some changes to their PDB Web Services interface. This change broke Mobile PyMOL's ability to search for and download PDBs. I haven't bothered to look at this specific situation but this a problem with many sites and automated interaction. NCBI has a nice eutils interface that has remained stable for a while, I'd been trying to get more groups to offer a web interface designed for automated interactions. FWIW, http://www.ncbi.nlm.nih.gov/books/NBK25500/ Do you have automated access to this library for example, http://www.ncbi.nlm.nih.gov/Structure/index.shtml they also have their own viwer, for example, http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml but pymol seems a bit more extensive. I have updated Mobile PyMOL and will soon resubmit it to the AppStore for verification and release. This process takes typically takes no less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users please use the following technique to acquire structures: (1) Using Safari on the iPad browse to the www.pdb.org and find the structure you want. (2) Click Download Files from the upper right hand side of the structure's page and then select PDB File (Text). (3) Click Open in PyMOL. Happily, as a long-term solution, I've established contact with the PDB Web Services Group and we'll now be made aware of future changes. The PDB is an extremely valuable resource in the community and I'm glad we could work this out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d ___ 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 -- LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d ___ 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] Stucked...
Date: Tue, 9 Oct 2012 03:07:08 +0200 From: ivan...@gmail.com To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Stucked... Dear PyMol users, I'm facing very unusual runtime problem. After successful compiling of PyMol 1.5.0.1 on Slackware64 13.37 (actually, this system is S64-current from February), and running pymol, program prompting several lines, and then goes in some sort of freeze state. I had a similar problem with that version - the freeze state occured after trying to load a single file and one core went to 100 percent although I can't remember if ctrl-C killed it or not. I finally used the configure/ make route which worked after significant patching ( including simple syntax errors). The output is: bash-4.1$ /opt/pymol-svn/pymol PyMOL(TM) Molecular Graphics System, Version 1.5.0.1. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at http://www.pymol.org;. Enter help for a list of commands. Enter help command-name for information on a specific command. Hit ESC anytime to toggle between text and graphics. Detected OpenGL version 2.0 or greater. Shaders available. Program hasn't any graphical, or further console prompt, and Ctrl+C can't terminate the app, the only way is with kill from another virtual console... That's it :( I hope someone knows what's the cause. -- If you don't care where you are, then you ain't lost -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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] I just built pymol, comes up but hangs on any attempt to view a test pdb.
From: jason.vertr...@schrodinger.com Date: Fri, 5 Oct 2012 09:36:29 -0500 Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. To: marchy...@hotmail.com CC: li...@cowsandmilk.net; pymol-users@lists.sourceforge.net Hi Mike, I suggest downloading the latest code, v1.5.0.4, from the open-source project page, if you want to build by hand. see comments in my last post, I think that is what I did. Although autoreconf may not have helped anything. I see the confusion now. We'll update SourceForge on our next release so that it says the latest is v1.5.0.5, not v1.5.0.1. To get the latest code, please do this: svn co https://pymol.svn.sourceforge.net/svnroot/pymol/root/pymol/trunk/pymol pymol To build, you need Python 2.7 or later and the process is very simple: sudo python setup.py install sudo python setup2.py install that was what created the first version I ran, it seemed fine until I tried to display a test pdb then it hung in 100 cpu on one core. What kind of computer is this? What video card do you have? Dell Laitittude, but this is probably due to other issues. I don't really recall what the first version said, I think it was hypothetical as in may need license etc. The version from ./configure had a whole bunch of problems- simple syntax errors like missing comma to no link to the ccealignmodule but once I kluged around the CGO problems I think I was on my own :) The make; make install setup was deprecated a long time ago which is why this didn't work. We use Python distutils to build, as you've found out. I never use python and I probably never would have gotten .1 to work if I had to deal with that :) I'm not sure of the rationale here but while you were phasing out a number of things I thought that make was just lagging, intended for developers. Anyway it seems fine now, although attempting to use fit on my 2 molecules gave a non-intuitive result I think the one was so mangled that it had problems aligning them. Glad it's working. Fit is a mathematically optimal superposition of vector sets. Are your atom pairings correct? If you want to specify them manually, check out Wizard Pair Fitting. If you send me the molecules I'm happy to take a look for you, too. Thanks, I have no idea. Naive overlap was a bit confusing but I'm dealing with simple things right now. I have 2 beta-carotene xtz files created from scripts, one from the mmcif files on pdb.org and another derived from jdftx after 300 position iterations using very simple C and H models. In any case, I think part of the problem is just using .53 for atomic/angstrom conversions but it looks like fit results were bizarre: the 2 ends of the molecule were in about the same place but the chains extended in opposite directions from there ( it wasn't immediately obvious if I created some wierd linking errors based on this behaviour LOL). Cheers, -- Jason On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka marchy...@hotmail.com wrote: CC: pymol-users@lists.sourceforge.net From: li...@cowsandmilk.net Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Date: Thu, 4 Oct 2012 22:03:59 -0400 To: marchy...@hotmail.com You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. Well, I thought there may be a dev list or something for the most of this stuff but in any case I'm on Ubuntu but that probably was not a big factor for some of the issues I ran into I just wanted to display 2 molecules side by side and could not get jmol or gdis to work right away and someone suggested this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn glut on cygwin but I imagine that would be an even bigger chore to port LOL). If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I think at some point I ran autoreconf -l thinking I could go the configure route but then did python setup.py build and install in separeate steps., This seemed to work but attempts to display the test pdb files never displayed anything, I could not get any more menu's and one core was running at 100 percent until I killed it. Going the confugre route, I think the first problem was with a bunch of undefined CGO things. but you can see the changes below. The EXT thing was spurious probably as there was a missing -lGLEW and I had to relink. This is obviously a raw dump of things that I tried along with stuff that ultimately worked but fwiw. marchywka
Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.
fwiw, I never figured out why the out-of-the-box build hung using the python approach but I went through the ./cogifure, make make install route and did get the test molecules to display. However, I ran into lots of problems with the ShaderMgr and ccealignmodule and then finally the link was missing -lGLEW. In any case it looks like I am all set but I thought the download would come closer to working right away. And the xyz files I wanted to display do appear to come up just great. So do I need a license for the open source version? Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency From: marchy...@hotmail.com To: pymol-users@lists.sourceforge.net Date: Thu, 4 Oct 2012 15:43:53 -0400 Subject: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Is there some common reason for this? CPU on one core stays at 100 percent and no more menu's come up. The larger window says at the bottom that the version is supposed to be licensed but I just pulled it down from sourceforge and not sure that this version needs a key to work. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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] I just built pymol, comes up but hangs on any attempt to view a test pdb.
.a layer4/.libs/liblayer4.a layer5/.libs/liblayer5.a -Wl,--no-whole-archive -L/usr/lib/x86_64-linux-gnu -Wl,--whole-archive -lGLEW -lGL -lGLU /usr/lib/x86_64-linux-gnu/libfreetype.so -lz -lpng -lglut -Wl,--no-whole-archive -ldl -O2 -Wl,-soname -Wl,libpymol.so.0 -o .libs/libpymol.so.0.0.0 #gcc -shared -fPIC -DPIC -Wl,--whole-archive contrib/uiuc/plugins/molfile_plugin/src/.libs/libmolfile_plugin0.a ov/src/.libs/libov.a layer0/.libs/liblayer0.a layer1/.libs/liblayer1.a layer2/.libs/liblayer2.a layer3/.libs/liblayer3.a layer4/.libs/liblayer4.a layer5/.libs/liblayer5.a -Wl,--no-whole-archive -L/usr/lib/x86_64-linux-gnu -lGL -lGLU /usr/lib/x86_64-linux-gnu/libfreetype.so -lz -lpng -lglut -ldl -O2 -Wl,-soname -Wl,libpymol.so.0 -o .libs/libpymol.so.0.0.0 marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ -David On Oct 4, 2012, at 9:22 PM, Mike Marchywka marchy...@hotmail.com wrote: fwiw, I never figured out why the out-of-the-box build hung using the python approach but I went through the ./cogifure, make make install route and did get the test molecules to display. However, I ran into lots of problems with the ShaderMgr and ccealignmodule and then finally the link was missing -lGLEW. In any case it looks like I am all set but I thought the download would come closer to working right away. And the xyz files I wanted to display do appear to come up just great. So do I need a license for the open source version? Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency From: marchy...@hotmail.com To: pymol-users@lists.sourceforge.net Date: Thu, 4 Oct 2012 15:43:53 -0400 Subject: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Is there some common reason for this? CPU on one core stays at 100 percent and no more menu's come up. The larger window says at the bottom that the version is supposed to be licensed but I just pulled it down from sourceforge and not sure that this version needs a key to work. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ 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
