Re: [PyMOL] Visualisation of protein-ligand interactions in pymol
Thomas, thanks this works perfect. Jason, I've tested this script on my system ( this is the membrane protein inserted in the bilayer surrounded by two water layers ( up and down ). During simulation individual water mollecules move into the protein interiour ( in that case protein like a water pore althought it's the receptor ) so I want to visualise only that buried water. I've tried to do it via find_buried_waters script both via ASA as well as in case when I've used small cutoffs ( 0.1) but the script selected too many waters ( e.g virtually all waters from up and down layers have been selected ). How I could specify this selection more carefully ? find_buried_waters 1, 0.1 James 2012/6/12 Thomas Holder spel...@users.sourceforge.net This will show them in the same slot in group mode. sorry, not group mode but grid mode of course. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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] clipping planes
Dear all, it is nice to set via mouse wheel the clipping. Is it possible to get this values somewhere out of pymol that one could use the actual values in a script? I find it a bit complicated and time consuming to play always a few times with the values in a script, to find values which looks fine. Best Regards Christian -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Script to calculate Fab elbow angle
Hello all - I'd like to share with you this script that I recently added (with Troels' help) to the PyMOL Wiki. http://www.pymolwiki.org/index.php/Elbow_angle Given a PyMOL object containing an antibody Fab fragment complex, light and heavy chain IDs for the Fab, and residue numbers for the boundary between variable and constant domains for each chain, the script will output the elbow angle of the Fab complex and optionally draw a representation of the vectors used to calculate it. It's under version control in the Pymol-scripts-repo, and any suggestions and/or fixes are welcome. Please note that elbow_angle requires transformations.py by Christoph Gohlke and com.py by Jason Vertrees, both of which are also available in the Pymol-scripts-repo. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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] clipping planes
Christian, you should be able to get the values from the tuple returned by get_view(). Looking into this would be a good starting point. from my old notes (origin unknown...): 0-8 is the 3x3 rotation matrix 9-11 is the camera location (I think -- been a while...) 12-14 is the origin of rotation 15-16 are the clipping distances and 17 is the orthoscopic flag. Cheers, Carsten -Original Message- From: Christian Roth [mailto:christian.r...@bbz.uni-leipzig.de] Sent: Friday, June 15, 2012 12:57 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] clipping planes Dear all, it is nice to set via mouse wheel the clipping. Is it possible to get this values somewhere out of pymol that one could use the actual values in a script? I find it a bit complicated and time consuming to play always a few times with the values in a script, to find values which looks fine. Best Regards Christian -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Script to calculate Fab elbow angle
Jared, Very cool script -- and beautiful visualizations. It's good to note that since it's in git-repo the new Plugin Manager can access it (just be sure to install COM and transformations, first). What used to take 3--5 minutes (downloading each script and putting them somewhere after cleaning up the text) now takes just seconds. Great work. Cheers, -- Jason On Fri, Jun 15, 2012 at 1:32 PM, Sampson, Jared jared.samp...@nyumc.org wrote: Hello all - I'd like to share with you this script that I recently added (with Troels' help) to the PyMOL Wiki. http://www.pymolwiki.org/index.php/Elbow_angle Given a PyMOL object containing an antibody Fab fragment complex, light and heavy chain IDs for the Fab, and residue numbers for the boundary between variable and constant domains for each chain, the script will output the elbow angle of the Fab complex and optionally draw a representation of the vectors used to calculate it. It's under version control in the Pymol-scripts-repo, and any suggestions and/or fixes are welcome. Please note that elbow_angle requires transformations.py by Christoph Gohlke and com.py by Jason Vertrees, both of which are also available in the Pymol-scripts-repo. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] GLSL Shaders
Hi Shiven, Thought some of you may be interested in this: http://pymolwiki.org/index.php/GLSL_Shaders Very nice work! Flexibility of representation and speed were the two main reasons we advanced to GLSL shaders over immediate mode rendering and display lists for PyMOL. Shaders offer powerful advances in rendering as you have shown. Thanks for posting this -- great screen shots. I hope others take some time to learn about shaders, too. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] 60-mer virus capsid (need computing power!)
Hi Shane, With PyMOL v1.5 and later, and a reasonable machine you should be able to use large systems (250,000, and upward of 1,000,000+ atoms) without much of a problem. Using the following simple test script: fetch 2xpj, type=pdb1, async=0 split_states 2xpj delete 2xpj orient For these 240,000 atoms on a Dell T5500 with a very nice video card, I get: * 30 FPS as lines * 28 FPS using cartoons * 30 FPS a ribbons * 30 FPS as surface For these 240,000 atoms on a (1 year old) MacBookPro (with ATI Radeon HD 6770) I get * 60 FPS as lines * 33 FPS as cartoon * 36 FPS as ribbon * 27 FPS as surface 30--60 FPS is surely in the realm of interactive. Earlier versions of PyMOL would have a tough time with these data. (Plus the new versions of PyMOL have nicer rendering in real time.) Next, you wrote: Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/A With Moore's Law still in effect, nothing is overkill. However, consider value for money: the recent announcements from Apple centered around the MacBookPro -- not the MacPro. It should be clear that those who financially support PyMOL are responsible for this level progress. The diff from v1.4 to v1.5 was in the range of 50,000+ lines -- and we couldn't have done that work without our supporters. So, a special thanks goes out to them! Cheers, -- Jason On Wed, Jun 13, 2012 at 2:32 PM, Shane Neeley shane.nee...@gmail.com wrote: Hi, Does anyone use pymol for very large structures, such as a full virus 60-mer capsid? If so, what processing power, memory, graphics card, etc. do you need to render these large files and manipulate them without any slowing? PyMol takes about 1 minute to think after trying to spin one of these full capsids, and that is on a dual-core 8gb ram laptop. Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/A Has anyone built other machines to do this sort of work? Appreciate your input, Shane Neeleu -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] 60-mer virus capsid (need computing power!)
Hi Jason, Thanks a lot for the performance info. I think that a full capsid would be around 300,000 atoms, so your info is very helpful. We will probably invest in the newest version of pymol when we purchase the computer. On Fri, Jun 15, 2012 at 12:19 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Shane, With PyMOL v1.5 and later, and a reasonable machine you should be able to use large systems (250,000, and upward of 1,000,000+ atoms) without much of a problem. Using the following simple test script: fetch 2xpj, type=pdb1, async=0 split_states 2xpj delete 2xpj orient For these 240,000 atoms on a Dell T5500 with a very nice video card, I get: * 30 FPS as lines * 28 FPS using cartoons * 30 FPS a ribbons * 30 FPS as surface For these 240,000 atoms on a (1 year old) MacBookPro (with ATI Radeon HD 6770) I get * 60 FPS as lines * 33 FPS as cartoon * 36 FPS as ribbon * 27 FPS as surface 30--60 FPS is surely in the realm of interactive. Earlier versions of PyMOL would have a tough time with these data. (Plus the new versions of PyMOL have nicer rendering in real time.) Next, you wrote: Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/A With Moore's Law still in effect, nothing is overkill. However, consider value for money: the recent announcements from Apple centered around the MacBookPro -- not the MacPro. It should be clear that those who financially support PyMOL are responsible for this level progress. The diff from v1.4 to v1.5 was in the range of 50,000+ lines -- and we couldn't have done that work without our supporters. So, a special thanks goes out to them! Cheers, -- Jason On Wed, Jun 13, 2012 at 2:32 PM, Shane Neeley shane.nee...@gmail.com wrote: Hi, Does anyone use pymol for very large structures, such as a full virus 60-mer capsid? If so, what processing power, memory, graphics card, etc. do you need to render these large files and manipulate them without any slowing? PyMol takes about 1 minute to think after trying to spin one of these full capsids, and that is on a dual-core 8gb ram laptop. Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/A Has anyone built other machines to do this sort of work? Appreciate your input, Shane Neeleu -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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
