Re: [PyMOL] command question RE printing out distances to text file
Hi Suzanne, You can also get the distance printed in the external GUI or terminal window by using the cmd.distance version of the command. So either you can assign the distance to a variable and print it or you can print the result directly. Assuming you have two selections, sele1 and sele2 specifying the atoms of interest you could do something like this: d = cmd.distance(sele1,sele2) print sele1,sele2,d Cheers, Rob On Mon, 2014-06-09 13:13 EDT, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Suzanne, you can use the get_distance command. It doesn't generate a distance object but prints the distance to the external window. http://pymolwiki.org/index.php/Get_Distance Cheers, Thomas On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: Fellow Pymol Users: I may have asked this question before...but if so have forgotten. I am measuring distances between 2 atoms in 2 different objects using the distance command, and it is working perfectly, but I wonder if there is a command I can use/add so that those distances can be printed in the external gui as well as being shown in the viewer. I will be doing lots of these at the same time and the screen will get crowded. Thank you in advance. -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://www.hpccsystems.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] command question RE printing out distances to text file
Hi Suzanne, You can also get the distance printed in the external GUI or terminal window by using the cmd.distance version of the command. So either you can assign the distance to a variable and print it or you can print the result directly. Assuming you have two selections, sele1 and sele2 specifying the atoms of interest you can do: d = cmd.distance(sele1,sele2) print sele1,sele2,d Cheers, Rob On Mon, 2014-06-09 13:13 EDT, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Suzanne, you can use the get_distance command. It doesn't generate a distance object but prints the distance to the external window. http://pymolwiki.org/index.php/Get_Distance Cheers, Thomas On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: Fellow Pymol Users: I may have asked this question before...but if so have forgotten. I am measuring distances between 2 atoms in 2 different objects using the distance command, and it is working perfectly, but I wonder if there is a command I can use/add so that those distances can be printed in the external gui as well as being shown in the viewer. I will be doing lots of these at the same time and the screen will get crowded. Thank you in advance. -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://www.hpccsystems.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] Pymol startup error
Hi, I am suffering from pymol startup error. It gets terminated with the following error messages: PyMOL(TM) Molecular Graphics System, Version 1.5.0.3. 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. *** buffer overflow detected ***: /usr/bin/python terminated === Backtrace: = /lib64/libc.so.6(__fortify_fail+0x37)[0x7f30e5ee8277] /lib64/libc.so.6(+0xfc350)[0x7f30e5ee6350] /lib64/libc.so.6(+0xfb7d9)[0x7f30e5ee57d9] /lib64/libc.so.6(_IO_default_xsputn+0x89)[0x7f30e5e623d9] /lib64/libc.so.6(_IO_vfprintf+0x48a3)[0x7f30e5e35473] /lib64/libc.so.6(__vsprintf_chk+0x97)[0x7f30e5ee5877] /lib64/libc.so.6(__sprintf_chk+0x7d)[0x7f30e5ee57bd] /usr/lib64/python2.7/site-packages/pymol/_cmd.so(CShaderMgr_ReadShaderFromDisk+0x2f3)[0x7f30e46ca8d3] /usr/lib64/python2.7/site-packages/pymol/_cmd.so(CShaderPrg_NewFromFile+0x2e)[0x7f30e46cb71e] /usr/lib64/python2.7/site-packages/pymol/_cmd.so(ShaderMgrConfig+0xa9)[0x7f30e46cb849] /usr/lib64/python2.7/site-packages/pymol/_cmd.so(was_main+0x13e)[0x7f30e49bb8ce] /usr/lib64/python2.7/site-packages/pymol/_cmd.so(+0x34b5c1)[0x7f30e497e5c1] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x113a)[0x7f30e646611a] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x143)[0x7f30e646b303] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xd27)[0x7f30e6465d07] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x403)[0x7f30e646b5c3] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7f30e64998b2] /usr/lib64/libpython2.7.so.1.0(+0xf3d91)[0x7f30e64a6d91] /usr/lib64/libpython2.7.so.1.0(PyRun_FileExFlags+0x86)[0x7f30e64a7156] /usr/lib64/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0x17d)[0x7f30e64a7a2d] /usr/lib64/libpython2.7.so.1.0(Py_Main+0x3ad)[0x7f30e64b122d] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f30e5e0ba15] /usr/bin/python[0x400791] === Memory map: 0040-00401000 r-xp 09:06 1181836 /usr/bin/python2.7 0060-00601000 r--p 09:06 1181836 /usr/bin/python2.7 00601000-00602000 rw-p 1000 09:06 1181836 /usr/bin/python2.7 00e65000-01a25000 rw-p 00:00 0 [heap] 404f9000-40596000 rw-p 00:00 0 41954000-41956000 r-xs 09:08 19 /tmp/gleT7vZR (deleted) 7f30dd223000-7f30dd423000 rw-s 7661eb000 00:05 593 /dev/nvidia0 7f30dd423000-7f30dd623000 rw-s 59aad7000 00:05 593 /dev/nvidia0 7f30dd623000-7f30dd823000 rw-s 6072fa000 00:05 593 /dev/nvidia0 7f30dd823000-7f30dd923000 rw-s 506579000 00:05 593 /dev/nvidia0 7f30dd923000-7f30dd92a000 rw-s 5176ff000 00:05 593 /dev/nvidia0 7f30dd92a000-7f30dd94a000 rw-s d006 00:05 593 /dev/nvidia0 7f30dd94a000-7f30dd98a000 rw-s 574b37000 00:05 593 /dev/nvidia0 7f30dd98a000-7f30dd9aa000 rw-s 56bbd3000 00:05 593 /dev/nvidia0 7f30dd9aa000-7f30dd9ea000 rw-s 6d1e49000 00:05 593 /dev/nvidia0 7f30dd9ea000-7f30ddaa2000 rw-p 00:00 0 7f30ddaa2000-7f30ddaa5000 r-xp 09:06 1058995 /usr/lib64/python2.7/lib-dynload/fcntl.so 7f30ddaa5000-7f30ddca4000 ---p 3000 09:06 1058995 /usr/lib64/python2.7/lib-dynload/fcntl.so 7f30ddca4000-7f30ddca5000 r--p 2000 09:06 1058995 /usr/lib64/python2.7/lib-dynload/fcntl.so 7f30ddca5000-7f30ddca6000 rw-p 3000 09:06 1058995 /usr/lib64/python2.7/lib-dynload/fcntl.so 7f30ddca6000-7f30ddcc1000 r-xp 09:06 1059009 /usr/lib64/python2.7/lib-dynload/_io.so 7f30ddcc1000-7f30ddec1000 ---p 0001b000 09:06 1059009 /usr/lib64/python2.7/lib-dynload/_io.so 7f30ddec1000-7f30ddec2000 r--p 0001b000 09:06 1059009 /usr/lib64/python2.7/lib-dynload/_io.so 7f30ddec2000-7f30ddecb000 rw-p 0001c000 09:06 1059009 /usr/lib64/python2.7/lib-dynload/_io.so 7f30ddecb000-7f30ddecf000 r-xp 09:06 1059019 /usr/lib64/python2.7/lib-dynload/zlib.so 7f30ddecf000-7f30de0ce000 ---p 4000 09:06 1059019 /usr/lib64/python2.7/lib-dynload/zlib.so 7f30de0ce000-7f30de0cf000 r--p 3000 09:06 1059019 /usr/lib64/python2.7/lib-dynload/zlib.so 7f30de0cf000-7f30de0d1000 rw-p 4000 09:06 1059019 /usr/lib64/python2.7/lib-dynload/zlib.so 7f30de0d1000-7f30de253000 rw-p 00:00 0 7f30de253000-7f30de25b000 r-xp 09:06 1058997 /usr/lib64/python2.7/lib-dynload/operator.so 7f30de25b000-7f30de45a000 ---p 8000 09:06 1058997 /usr/lib64/python2.7/lib-dynload/operator.so 7f30de45a000-7f30de45b000 r--p 7000 09:06 1058997 /usr/lib64/python2.7/lib-dynload/operator.so
Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
Hi Darrell, Thanks for the suggestion. To make a long story short, we're publishing a new a method to assign secondary structure elements (SSE) solely from the C-alpha atoms (with ~95% accuracy relative to DSSP). We've compared this to backbone reconstruction schemes and the time to rebuild the backbone atoms is simply too time consuming (about an order of magnitude). In fact, the BBQ method claims to be fast but, based on my estimates, it's actually about twice as slow as the optimized rebuild program (when optimized to only rebuild the backbone atoms using basic geometry) from the MMTSB Tool Set by Michael Feig et al. Anyhow, my collaborator wanted to write a PyMOL plugin which will assign the SSEs using our program (for each state) and then display them nicely in PyMOL. This doesn't seem to be possible in PyMOL without reconstructing the backbone atoms. Yes, we can color each SSE accordingly but I was hoping that there was a better solution. Best, Sean From: darre...@niaid.nih.gov To: magic...@hotmail.com; jared.samp...@nyumc.org CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure Date: Wed, 4 Jun 2014 21:18:27 + Hi Sean, If you're doing this for illustrative purposes, why not just build the inferred backbone? You could use BBQ, among many others: http://biocomp.chem.uw.edu.pl/tools/bbq FWIW, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Pagehttp://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor Twitter: @niaidbioithttps://twitter.com/niaidbioit Disclaimer: The information in this e-mail and any of its attachments is 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. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Sean Law magic...@hotmail.commailto:magic...@hotmail.com Date: Wednesday, June 4, 2014 4:17 PM To: Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org Cc: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure Jared, For now, we are using different colors to indicate the SS assignments but it's not pretty. We would prefer to show the SS for both sheets and helices. Can you elaborate on what you mean by radially symmetric. Are there other cartoon modes where I would be able to get both helices and sheets after altering the residue's SS assignment by hand? I see what you mean by not being able to define the flat plane though. Best, Sean From: jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org To: magic...@hotmail.commailto:magic...@hotmail.com CC: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure Date: Wed, 4 Jun 2014 20:03:54 + Hi Sean - I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s part. Rather, I think it may have something to do with two facts: 1) unlike loops, sheets represented in automatic mode are not radially symmetric; and 2) unlike helices, the orientation of the sheet at a particular CA atom cannot be determined by its immediate neighbors. I haven’t had a chance to look at the relevant source, so I can’t confirm this at the moment, but it seems likely to me that PyMOL uses the other (non-CA) backbone atoms to define the “flat” plane of a sheet, and without this information, instead of guessing at its orientation, it omits the sheet entirely. (This also appears to be the case for other non-radially symmetric modes, including dumbbell, rectangle, and oval.) Could you get by using different colors to indicate your SS assignments in another cartoon mode? Cheers, Jared Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jun 4, 2014, at 1:50 PM, Sean Law magic...@hotmail.commailto:magic...@hotmail.com wrote: Hi PyMOLers, I have a c-alpha only model and I would like to visualize both helices and sheets based on my own custom SS assignments (via alter). Altering a residue's SS assignment to helix or loop (ss=H or ss=L) is fine and can be visualized. However,
Re: [PyMOL] command question RE printing out distances to text file
Thank you Robert and Thomas--I will try both and see what works best for my needs. From: Robert Campbell [robert.campb...@queensu.ca] Sent: Monday, June 09, 2014 10:04 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] command question RE printing out distances to text file Hi Suzanne, You can also get the distance printed in the external GUI or terminal window by using the cmd.distance version of the command. So either you can assign the distance to a variable and print it or you can print the result directly. Assuming you have two selections, sele1 and sele2 specifying the atoms of interest you can do: d = cmd.distance(sele1,sele2) print sele1,sele2,d Cheers, Rob On Mon, 2014-06-09 13:13 EDT, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Suzanne, you can use the get_distance command. It doesn't generate a distance object but prints the distance to the external window. https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distancek=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b Cheers, Thomas On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: Fellow Pymol Users: I may have asked this question before...but if so have forgotten. I am measuring distances between 2 atoms in 2 different objects using the distance command, and it is working perfectly, but I wonder if there is a command I can use/add so that those distances can be printed in the external gui as well as being shown in the viewer. I will be doing lots of these at the same time and the screen will get crowded. Thank you in advance. -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.ca https://urldefense.proofpoint.com/v1/url?u=http://pldserver1.biochem.queensu.ca/~rlck=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=aaad7877cf1640401ae708b7b5f5a2fbe03abec4d2f0ef509e7360c0017ee225 -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration https://urldefense.proofpoint.com/v1/url?u=http://www.hpccsystems.com/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=dabd029c6435c0bbe92d916555213bd7ccbd3d4ac6dcf2de28cf19c428ff0eed ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/pymol-usersk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=6e6df3376d82f34b3bce9c1de38053ec6052ce7313087062131127d0c0c03fb7 Archives: https://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/pymol-users%40lists.sourceforge.netk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=f7df11447d13070db8093ed0604c19654bebcf07d28d46919253043bb5dbe80e -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ 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
