Re: [PyMOL] Student version
FYI, Pymol runs nicely on modern Chromebooks. You can install Pymol easily in the Linux container using *sudo apt install pymol*. I think the latest apt version is 2.4. CCP4i/Coot also runs nicely in the Linux container. (I'm using a Lenovo Flex 5i Chromebook, $320, as a test bed. This system has an Intel i3 CPU.) An Intel Chromebook might be an attractive option for undergrads for biochemistry classes and/or protein crystallography research projects. You can install Pymol in Windows with pip as well. Roger Rowlett Gordon & Dorothy Kline Professor, Emeritus Department of Chemistry Colgate University On Fri, Oct 6, 2023 at 5:49 AM Thomas Charles Pochapsky < pocha...@brandeis.edu> wrote: > Hi, all. Did anybody ever reply about the student version of PyMol > downloads? I use it in my class on a regular basis, but I can no longer > find the link on the Schrodinger web site. There is a free download for > Maestro, with which I am unfamiliar. Is this a replacement? > > Thanks. Tom > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] CCP4 maps not aligning to my PDB file
One way of displaying CCP4-generated maps in Pymol is described on this web page: https://sites.google.com/colgate.edu/xrd-protocols/home/visualization-of-protein-models One way of generating CCP4 maps suitable for use in Pymol is described on this page: https://sites.google.com/colgate.edu/xrd-protocols/home/model-building-and-validation Roger Rowlett On Mon, Apr 12, 2021, 2:35 AM shubhashish chakraborty < cshubhash...@gmail.com> wrote: > Hello, > I am not able to align my pdb file with its respective electron density > map generated by CCP4i. Kindly let me know what is going wrong. > An image is attached for better reference. > > Thank you > > Shubhashish Chakraborty > PhD Research Scholar (SRF) > Varma Lab > Structural and Molecular biology Lab > Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) > Khargar, Navi Mumbai > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to see a homotetramer
fetch 6h07, type=pdb1 Roger Rowlett Gordon & Dorothy Kline Professor, Emeritus Department of Chemistry Colgate University On Tue, Jan 14, 2020, 3:42 AM Clelia Canova wrote: > Hi! > > I’m studying the file *6H07. pdb *for a project, download for rcsb.com. > How can I see the Biological Assembly on Pymol like in PDB, instead of > seeing only the monomer (asymmetric unit). > > In the screen I see 6h07 1/4 and not 4/4. > > In the commander zone it’s written: > ” Detected 4 cpu cores. Enable multithreaded rendering.” > If I push the key PLAY the protein start to move fast from 1 to 4 of 4 > positions. > > How can I see the 4 position together?? > > Thank you very much, > > Clelia Canova > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] distance wizard
You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1, etc.) ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 10/12/2017 2:18 PM, Leigh M wrote: Anyone know how pymol calculates distance between two atoms? I wrote a python script that calculates distance using the distance formula and the xyz coordinates in the pdb, and it differs from the wizard by ~40%. Any ideas on what might be going on would be helpdul Thanks! Leigh -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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
Clarisa, Depending on what you want to do with the file, you may not need to save a new PDB at all. You could for example, * Issue the command symexp ,,(all),4.0 to generate nearby symmetry mates, then remove the objects you don't need to form the proper dimer. ( is your PDB file object) * The select File...Save Molecule and select all the objects to save using shift-clicks. (but this may be unnecessary--see below) When you do this both chains will have the same chain identifers (e.g. chain A) This could be clumsy later if you are doing further manipulations of the structure and you save the molecule as a single PDB with two identical chain identifiers. In this case, every selection you made would be a double selection (one in both chains.) You can change the chain identifier for the symmetry chain easily enough in a text editor, I suppose, but this is an extra step. Alternatively, if you simply want to work with your new dimer structure in Pymol, there is no need to alter the chain numbers after doing the proper symmetry expansion. Rather, you can select individual items in one chain or the other by selecting the original or symmetry object. This might be useful, for example, if you want to highlight one active site and its interaction with the neighboring chain. I usually assign object names to the two monomers as "achain" and "bchain" to make manipulation of the structure easier. So, for example, * "Select asite, resi 42+44+98 and achain" might select active site residues from the original chain * "Select otherres, resi 33 and bchain" might select interactigin residues form your symmetry expanded chain. * No need to save the molecule as a separate PDB. Just save the session file. Cheers, ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 10/7/2015 11:00 AM, Clarisa Alvarez wrote: Hello everyone: I need help because I have a pdb of a monomer but I know that it is a dimer by crystallographic symmetry, how can I make a new molecule of it? because I could make it by generate/symmetry mate...but I could not save it...any help will be great! Thanks in advance! -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] animation showing conformational change
You can also do this locally on your own machine if you arrange to get the CNS morph_dist.inp script. (You need CNS to run it, of course.) The nice thing about this method is that it minimizes the structures of the intermediate morphs into something sensible. I don't know how sophisticated PyMols morphing command is, but some morphing programs simply do a linear interpolation between the starting and ending states, and that will lead to serious distortion of side chain and main chain geometries. The CNS morphing script will sort these out. The final morph, while not rigorously computed pathway between state 1 and state 2, is nevertheless a useful and possibly realistic pathway between states. The general steps to do this are: 1. Align the PDBs of the 2 states with your favorite software (Pymol super works OK), otherwise morph will include both translation and rotation 2. PDBs must have the same exact sequence homology: edit mutations to match WT 3. Run PDBs through a program to renumber atoms and residues. Both Res# and Atom# must begin with 1 4. Edit the CNS morph script for initial, final PDBs and # output frames 5. Run CNS script 6. Load PDBs into pymol and make your movie (creates list of PNG files) 7. Use ImageMagick to convert and animate a GIF. You can add introductory frames to the beginning and post-transformation frames at the end using ImageMagick. Maybe there is an easier way now but this is how I have done it before. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 4/9/2014 12:45 PM, Schubert, Carsten [JRDUS] wrote: Alternatively you could try the Morph server in Gerstein's lab and then load each intermediate structure into a separate state for animation purposes. http://morph2.molmovdb.org/ HTH Carsten *From:*Sampson, Jared [mailto:jared.samp...@nyumc.org] *Sent:* Wednesday, April 09, 2014 12:34 PM *To:* sunyeping *Cc:* pymol-users *Subject:* Re: [PyMOL] animation showing conformational change Hi Yeping - With incentive PyMOL version 1.6 or later, you can use `morph`. From what I read at http://pymolwiki.org/index.php/Morph, you'll need to put both conformations of the protein into one object, as different states. See http://pymolwiki.org/index.php/Load for more info on that. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Apr 9, 2014, at 11:58 AM, sunyeping sunyep...@aliyun.com mailto:sunyep...@aliyun.com wrote: Dear all, If I have the structures representing two conformations of one protein, then could I make a animation movie that shows how the protein transforms from one conformation to the other conformation using pymol? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net mailto:PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ 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 -- Put Bad Developers to
Re: [PyMOL] how to set different dash colors for the distance measurements
How about, color measure01, red color measure02, yellow etc. Roger Rowlett On Dec 24, 2013 8:51 AM, Li Xue me.li...@gmail.com wrote: Hello all, Is it possible that I could use *different* colors for the dashes for the distance measurements? I know I can use set dash_color, red to set all distance dashes into red. Many thanks. Li -- Xue, Li Post-doctoral Research Associate College of Information Sciences and Technology Penn State University Email: me.li...@gmail.com Web site: http://www.cs.iastate.edu/~lixue/ -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/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] PyMol graphics problem in Ubuntu 13.10, ATI Radeon HD 4650
You can try installing the ATI proprietary driver (fglrx, Catalyst) instead of using the open source driver that come with Ubuntu. Check to see if this driver is compatible with your card. I've had nothing but trouble and bad luck getting ATI graphics cards to work under linux. If building from scratch, I install an NVidia graphic card. Their proprietary drivers seem to have fewer problems. You can get a capable GeForce card for $30-$40 if you don't want 3D stereo. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 11/26/2013 10:51 AM, Hitesh Patel wrote: Hello all, I installed ubuntu 13.10 on my PC. It has ATI Radeon HD 4650 graphics card. When I am trying to load a pdb file in PyMol, It gives following error. Which drivers do I need to install? *EE ../../../../../../src/gallium/drivers/r600/r600_state.c:2373 r600_adjust_gprs - ps vs shader require too many register (109 + 20) for a combined maximum of 128 EE ../../../../../../src/gallium/drivers/r600/r600_shader.c:1580 r600_shader_from_tgsi - GPR limit exceeded - shader requires 128 registers EE ../../../../../../src/gallium/drivers/r600/r600_shader.c:158 r600_pipe_shader_create - translation from TGSI failed ! EE ../../../../../../src/gallium/drivers/r600/r600_state_common.c:754 r600_shader_select - Failed to build shader variant (type=1) -12 EE ../../../../../../src/gallium/drivers/r600/r600_state.c:2373 r600_adjust_gprs - ps vs shader require too many register (109 + 20) for a combined maximum of 128 * Thanks, Regards, Hitesh Patel -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/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] Select different set of atoms in different molecules
What about the following commands: select mystuff, resi 1-3 and m1 select otherstuff, resi 7-9 and m2 Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 9/5/2013 3:40 PM, Alessia Visconti wrote: Dear pyMOL users, I'm puzzled about how to solve an apparently simple task. I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select two different sets of atoms from each of them. Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] from m2. I tried several combinations of load and select, but no option worked. The last selection is always applied to both molecules. I also Googled it, without any success. Does anyone know if its possible to make a selection in isolation over a given molecule? Any suggestion will be highly appreciated! Thanks in advance, Alessia -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/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 -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/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
[PyMOL] Pymol 1.6.0.0 setup.sh issue
When executing setup.sh to create the pymol executable link the following error is encountered: start of snip Creating ./pymol startup script with PYMOL_PATH=/usr/local/xtal/pymol-1.6.0.0 If you need to move PyMOL in the future, re-run ./setup.sh afterwards. You may now want to copy or link: /usr/local/xtal/pymol-1.6.0.0/pymol to something like /usr/local/bin/pymol Enjoy! ./setup.sh: 45: ./setup.sh: Syntax error: ( unexpected (expecting done) end of snip When running the symlink a libglut link error occurs: /usr/local/xtal/pymol-1.6.0.0/pymol.exe: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory The pymol 1.5.0.3 shell script and symlink works fine. Running Ubuntu 12.04 LTS. Any ideas? Cheers, ___ Roger Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-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] morphing 3-states
ImageMagick can easily append/adjoin animated gifs. Roger Rowlett On Nov 24, 2012 8:38 PM, Jordan Willis jwillis0...@gmail.com wrote: Hi, I have 3 different conformations of the same structure and I was wondering what is the easiest possible way to morph 3 conformations. Morpheasy works fantastic for two conformations, and this makes around 80 frames. I can then reinitialize and do the other two states. I have no idea how to link the two. Does anyone have any ideas or documentation on this? Thanks, Jordan -- 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] 3D projector for low cost 3D Protein Cave
I'm using an older DepthQ-WXGA system and Quadro FX3700(?) graphics card in a classroom setting and it seems to work fine. Stunning, really. It uses a VGA cable and the 3-pin mini-DIN on the graphics card. I mount the IR emitter on top of the projector and everyone in the room can sync with it from IR reflected from the projection screen. For really long VGA cable runs, the syncing can blank out for a few seconds periodically, but for a typical short cable run (12 feet or so) the image is rock solid. You can mirror the projector display on a computer monitor from a VGA output port on the rear of the projector. Uses inexpensive LCD shutter glasses. The newer DepthQ models can utilize a larger number of video cards and obtain sync signals through the USB port with the appropriate NVidia drivers. I haven't used the newer models, but it sounds simpler to install. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 6/13/2012 1:48 PM, mesters wrote: Hi, I am planing to purchase/build a LOW-COST 3D Protein Cave consisting of a 3D capable projector (720p @ 120Hz or DLP 3D Ready?) and a windows 7 computer with a quadro 2000 card. However, I am a bit sceptic about the sync problem causing ghosting. Main Questions: 1) Is anyone out there succesfully operating a 3D projektor (with true stereoscopic 3D at 720p @ 120Hz) that has ist own 3-pin vesa out (!) to drive the nvidia emitter (like modern 3D-TVs do)? This would be the best solution to avoid ghosting (i.e. the output device drives the glasses, not the video card)! 2) Is anyone out there succesfully running a 3D projektor using the DLP Link option (white flash in between images to sync the glasses). Is this technique being used at all (for true stereoscopic 3D software such as Pymol, Coot, Yasara, etc.) by anyone? Optional: 3) What about the new 3D Monitors with a build-in IR emitter. Do those work well for 3D steroscopic viewing with software like Pymol? Any input is welcome, I do not want to spend a lot of money to find out it does not work after all Jeroen. -- 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] Electron Density
I think the isomesh command will let you set whatever contour level you wish, e.g.: isomesh map, mymap.map, X.X, maparea Where map is the name of the mesh object, mymap.map is the map file name, X.X is the desired contour level, and maparea, is the selection about which you would like to see the electron density mesh. I haven't tested the contour limits, but it's larger than 10. ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 12/5/2011 12:49 PM, Manas Sule wrote: I have tried that...but i can see the density in coot at even 8 sigma.. however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map Can u suggest any method to see the same density at 6 sigma Manas On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer pame...@mcw.edu wrote: isomesh [mesh name], [map name], 6.0 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ 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] about Display CCP4 Maps
Lina, If you want to create an "omit" map for your ligand using CCP4i, you can find instructions here for both Fo-Fc and 2Fo-Fc maps: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac To display an omit map in Pymol around your ligand, you can find instructions here: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps These last instructions are the same as those I posted on the CCP4 wiki. http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps __ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu Thomas Holder wrote: Hi Lina, do you already have any electron density or reflection file (*.map, *.mtz, ...) or do you want to create a "fake" density from your structure? It's not clear from your question. Cheers, Thomas On 10/25/2011 10:28 AM, lina wrote: Hi, I went through the pymolwiki and cross this page: http://www.pymolwiki.org/index.php/Display_CCP4_Maps I have some questions: 1] do I need generate the map from ccp4 (I have already installed the ccp4i, but seems not easy to know how to get the map) 2] For small molecular (ligand), the ccp4 is the best way to obtain its electron density map? Seems those questions are not so-pymol-related, but I wish if someone are familiar with this, can give me some advice?? Those questions might be easy, but to me at present it seems very confusing. Thanks with best regards, -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-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
[PyMOL] PUI session at 2012 ACA meeting
Pymol-ers, I am writing to alert the Pymol community that I will be co-organizing (under the auspices of the Council on Undergraduate Research) a session at the 2012 American Crystallographic Association meeting (July 28-Aug 1) devoted to practical aspects of developing X-ray crystallography at a predominantly undergraduate institution (PUI). A portion of this session will be devoted to protein X-ray crystallography. This session may be of interest to faculty at PUIs who are conducting protein X-ray crystallography, or are contemplating setting up a laboratory to conduct protein crystallography with undergraduate researchers. The session may also be of interest to individuals who are contemplating seeking faculty positions at PUIs and would like to know more about the challenges and successes of protein crystallography at PUIs. The session is still in the planning stages, but I anticipate the formal session will address instrumentation acquisition (aka external funding), undergraduate research training, and crystallographic pedagogy. We expect to have an exceptional panel of presenters that will also provide informal networking opportunities during the meeting. I am interested in hearing faculty at PUIs who are currently active in protein X-ray crystallography, and might be interested in attending or applying to be a presenter in this special meeting session. If you are currently conducting protein X-ray crystallography at a PUI, shoot me an email. Cheers, -- Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2___ 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] Visualizing protein-ligand complexes of metalloproteins
Visualizing the coordinated bonds are easy, e.g., select zn, resn zn (this would select the metal) show sticks, zn (this will show bonds to any atoms withing bonding distance of zn that are also shown as sticks) Additional bonds to heteroatoms may have to be manually added using the bond command. See the pymol wiki for how to select atoms to link with the bond command. You will have to show sticks to see the bond. Waters are usually visualized as spheres, and you may want to modify their vdw radius to 0.5-1.0 A to make them small enough. Cheers, Roger Rowlett On Apr 18, 2011 5:48 PM, Prija Ponnan prija.pon...@gmail.com wrote: Hello I am trying to visualize a protein-ligand complex of a metalloprotein using Pymol. The ligand and certain amino acids are coordinated with the metal ions in the binding site.The binding site also have some water molecules which are also making interactions with amino acids and the metal ions. But using Pymol i am not able to visualize the coordinated bonds. When I am visualizing the binding site of this protein using Pymol, the water molecules are showing multiple hydrogen bonds (6 hydrogen bonds), which is not correct according to the valency of oxygen. Please help me Thanks Prija Ponnan Research Student Department of Chemistry University of Delhi Delhi-110007, India Canadian Commonwealth Scholarship Program Scholar College of Pharmacy and Nutrition University of Saskatchewan Saskatoon,SKN5C9,Canada -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4
This appears to be a common problem with 1.4 and Jason is aware of it. The same issue exists in Ubuntu 9.04 with Nvidia 180.xx drivers, 32 bit. The Win version works OK. Roger Rowlett On Mar 29, 2011 7:53 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Joachim, I'm running into the same issue on a SuSe SLED10 box. The 32bit binary (on the 64bit OS) displays the same behavior, i.e. only the MESA libs were used. The 64bit version actually core dumps during startup. I opened up a bug report with Schrodinger and they were already working on it (I suppose the crash), but wouldn't hurt to reinforce the fact that the 32bit version only uses the MESA libs (under SuSe?). Good that your tried the more recent drivers, I was planning to do that but haven't got around to do this yet. Cheers, Carsten -Original Message- From: greipel.joac...@mh-hannover.de [mailto:Greipel.Joachim@mh- hannover.de] Sent: Tuesday, March 29, 2011 7:16 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4 Dear pymol users, pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA drivers (260.xxx and 270.xxx) does not recognize the OpenGL Version correctly. As a result there is a kind of software OpenGL used. The NVIDIA drivers provide OpenGL 3.3.0 but pymol 1.4 complains: Detected OpenGL version prior to 2.0. Shaders unavailable. OpenGL graphics engine: GL_VENDOR: Brian Paul GL_RENDERER: Mesa X11 GL_VERSION: 1.5 Mesa 6.4.2 This leads to a malfunctioning hardware stereo and renders pymol 1.4 unusable for us. Earlier pymol versions do not show that strange behavior. Other programs use the NVIDIA drivers perfectly well and allow displaying structures in hardware stereo. I tried this thing on several machines with the same result. Does anyone have a hint? Regards, -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350 Carl-Neuberg-Str. 1 30625 Hannover Germany Fon: +49-511-532-3718 Fax: +49-511-532-8924 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ 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 no longer fetches from pdb
Has anyone else noticed that Pymol (v 1.3 or 1.4) will no longer fetch data from the pdb server? If I issue 'set fetch_host, pdbe' I can fetch data OK, but if you 'set fetch_host, pdb' I'm getting a fetch error for any accession number. -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ 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 no longer fetches from pdb
Thanks, all. Looks like I'll have to investigate local issues with our institutional firewall. Sigh. Not the first time... Roger Rowlett On Mar 22, 2011 12:58 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Great, thanks, David. Just ensuring the problems been isolated. Cheers, -- Jason On Tue, Mar 22, 2011 at 9:53 AM, David Hall li...@cowsandmilk.net wrote: Resolves fine for me. -David On Mar 22, 2011, at 12:30 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Roger, On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett rrowl...@colgate.edu wrote: Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.organd it is currently generating a cannot be found error. I'll investigate further. This may be the issue with pymol if it is using that server path. This is clearly the reason for the error. PyMOL looks for PDBs at the main PDB site at the following path: ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/ and then appends the appropriate extension, which resolves and lists PDBs just fine (from my machine). Is anyone else having this error or just Roger? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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 Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ 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 1.4 OpenGL issue with Ubuntu 9.04
When Pymol 1.4 is started in Ubuntu 9.04 with the latest available Nvidia driver for this OS (version 180) I get the following startup error (and strange window rendering where bits of the pymol rendering window are transparent): "Detected OpenGL version prior to 2.0. Shaders unavailable." The detected GL_VERSION is 1.5 Mesa 6.4.2 Is there a way around this issue? Didn't seem to be a problem with Pymol 1.3.1. I don't see an obvious way to update OpenGL (manual install of newer Nvidia driver?). I'm not quite ready to upgrade to Ubuntu 10.04 LTS. Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ 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] Ubuntu 10.04 and pymol 1.4
In pymol 1.4, I get a strange error in Ubuntu 10.04 (VM): "pymol.exe: error while loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory" The file is there, and is readable. Any ideas? I have run ./setup.sh to establish all the correct environment variables. No problem running pymol 1.3.1 in the same VM (other than the missing binary graphics driver). Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ 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] cd in windows
David, Use double quotes or start typing and autocomplete with the tab key. Cheers. On 9/20/2010 11:20 AM, David A. Horita wrote: Hi, How does one change directories in Windows when the directory name has a space in it? I've tried double and single quotes as well as backslash space (I'd like to run a script that's in such a directory). Thanks David - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ 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 -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ 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] Calcium radius
FYI, the ionic radius of Ca(2+) is 1.14 A. A calcium atom is 1.80 A. After issuing the "alter elem ca, vdw=1.14" command, you may have to execute the "rebuild" command to change the previously displayed sphere radius. Cheers. On 3/16/2010 11:31 AM, Jason Vertrees wrote: Raluca, Here's how you would figure this out in PyMOL: # fetch a calmodulin fetch 1cll # print the calcium's vdW radius iterate first elem CA, print vdw which outputs 1.7995232. Due to numeric precision, that's 1.80. :-) I've seen it as 2.0 elsewhere. If you want to change the value, # alter all Calciums to have vdw radius X alter e. CA, vdw=X where X is your new radius. Cheers, -- Jason On Mon, Mar 15, 2010 at 7:47 AM, Raluca Mihaela ANDREI r.and...@sns.it wrote: Hi! I have a pdb file that contains Calmodulin protein with Calcium ions. I want to calculate the surface. Does anyone know which is the radius of Calcium in PyMOL library and were I can find this libray? Thank you, Raluca -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] New Feature Ideas
Two items come to mind: 1. A Powerpoint plugin for live Pymol viewing in presentations. 2. A simpler method of doing structure morphs in Pymol. Intelligent morphing is incredibly powerful for visualizing protein conformational changes based on "endpoint" protein structures, or just evaluating/understanding the differences between point mutations of proteins. I think both of these were on the radar screen for Pymol feature enhancement at some point in the recent past. Cheers. On 1/19/2010 11:26 PM, Jason Vertrees wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put "PyMOL" in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-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
[PyMOL] DepthQ configuration in a classroom setting
Has anyone on the board configured a DepthQ projector for classroom use, i.e. using a ceiling-mounted projector. Our IT department has recently installed a DepthQ projector in a classroom-type setting, and it displays stereo Pymol images for about 20 seconds, then loses sync. My configuration is the following: Intel WinXP PC with Quadro 3700 running NVidia driver 191.00 Stereo "ON" enabled in the Global settings of the Nvidia Control panel DepthQ installed as only graphical display device (currently) Screen resolution set to the native resolution of the DepthQ projector I'm running a recent version (1.2) of Pymol I assume that to get a second monitor display of the DepthQ projector I should attach a VGA cable to the "video out" port of the DepthQ and run that to an appropriate LCD monitor. Am I missing anything? I'm wondering if the video cabling is too long or inappropriate, causing the sync dropouts, or if I have missed something really elementary in the Nvidia configuration. At this point, I'm considering breaking down the classroom installation and testing the computer and projector on the bench. Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Caver 2.0.003 plugin
Has anyone got the Caver 2.0.003 plugin working in Ubuntu 9.04? I can install the plugin in pymol, load the example pdb (1MJ5) and open the dialog box, which seems to have the correct paths to the plugin .jar and lib directory. I can even select the correct starting point and have it displayed in pymol. However, when I click on compute tunnel, I get the error dialog box with: Error: 1 type 'exceptions.RuntimeError' Exception in Tk callback Function: function lambda at 0xb024c6c (type: type 'function') Args: () Traceback (innermost last): File /home/rrowlett/pymol/ext/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /home/rrowlett/pymol/ext/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /home/rrowlett/pymol/ext/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /home/rrowlett/pymol/modules/pmg_tk/startup/Caver2_0_003.py, line 429, in execute self.CreateDirectory(outdir) File /home/rrowlett/pymol/modules/pmg_tk/startup/Caver2_0_003.py, line 504, in CreateDirectory . . . etc. Same result in pymol 1.2r0 or 1.2b5 The Windows version works OK, but it would be nice to have my Linux workstations work, too. -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu -- ___ 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] Disabling cartoon_highlight_color
How do you disable cartoon_highlight_color once it has been enabled? The command "set cartoon_highlight_color, off" does not work in 1.2b3, as suggested by the Pymol wiki. Pymol just reports that "off" is not a color. Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] (Simple) unit cell construction
Is there a relatively simply way to get pymol to populate a unit cell with exactly the correct number of copies of the asymmetric unit, i.e., similar to the Uppsala software factory utility XPAND or the "Build Crystallographic Symmetry" command in SPDBV? Ideally, it would be helpful to perform the symmetry operations on the ASU, and then have the ability to translate errant symmetry copies by +/- a,b, or c to get an intelligent packing of the unit cell box. The "symexp" command is contact-distance controlled, and is better for inspecting crystal packing than for creating nice "fluff" images of unit cells. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
Re: [PyMOL] Saving figures for publication
DPI is a function of print size and image pixel dimensions. Pymol or any other program that displays graphics does not have a dpi. The 72 dpi you are referring to is a typical (for some systems) display resolution in pixels per inch. If your journal figure is going to be 3 x 3 inches, for example, you will need to provide an image of 1800 x 1800 pixels to achieve the required 600 dpi. Roger Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu -Original Message- From: Abhinav Kumar abhin...@slac.stanford.edu Date: Friday, Mar 13, 2009 6:03 pm Subject: [PyMOL] Saving figures for publication To: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Hi, I need to make figures in tiff format with at least 600 dpi resolution as required by the journal. The default resolution in Pymol figures is 72. Is there a simple way to increase the resolution (and save it in tiff format)? Alternatively, I can 'convert' from png to tiff afterwards -- Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] How to view electron densities from the PDB
Robert Campbell wrote: Hi, On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com wrote: This is probably a fairly basic question, but I'm stumped. I want to visualize electron densities along with my PDB file. So, say I'm interested in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL doesn't seem to read the CIF file (?), so I downloaded and installed the PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html). I tried sf-convert -i CIF -o Xplor -sf 2djx-sf.cif but got some errors about the input format. sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif seemed to work (it produced a .Xplor file with what looks like data to me). However, PyMOL gives me errors when I try to load the resulting .xplor file. The sf file that you have is not electron density but structure factors. You need to calculate electron density from the data in that file and phases, which you would have to calculate from the structure. Fortunately someone else is already doing that for you. Try the Electron Density Server (http://eds.bmc.uu.se/eds/). Simply enter the PDB code and you'll find ... oh dear ... that 2djx is not entered yet. :( I see that it is a fairly new structure (released yesterday) and EDS is updated weekly. So either wait a week or so, or find a crystallographer to run the coordinates and structure factors through a single refmac cycle to calculate a map for you. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Instructions for creating and displaying CCP4 maps in pymol can be found at http://www.pymolwiki.org/index.php/Display_CCP4_Maps. However, displaying a model with maps in pymol is perhaps not the most straightforward way to inspect models and maps. Even here, you will have to use the fft utility in CCP4 to generate the maps. (You will probably want to display a simple map.) To generate a CCP4 map, you will have to convert your mmCIF file to an appropriate MTZ file using another CCP4 utility. It might be more straightforward to read in the PDB file and the appropriate MTZ file into Coot instead of pymol. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
Re: [PyMOL] Graphics Workstation
Buz Barstow wrote: Dear All, I'm considering purchasing a new graphics workstation for molecular graphics and macromolecular refinement. I'm considering buying a machine with 2 quad core xeon processors, and a nVidia Quadro FX graphics card with 1.5 Gb of memory. Can the current generation of software, and maybe the next generation of visualization software, make use of a system with so many processors, or am I better off spending the money elsewhere? Thanks! and all the best, --Buz - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Pymol will use all 4 cores of my Q9300 processor, but most XRD applications (CCP4, O, EPMR, etc.) will only use one core at a time currently. Of course, with more cores, you can run more jobs at once without significant penalty (depending on how memory- or disk-bound they are). I built my last Linux workstation around a very inexpensive DG35EC Intel motherboard and a value-oriented Intel Q9300 quad-core CPU, and attached a 9600GT graphics card (non-stereo-enabled) and a 24 LCD panel. For less than $1500 this configuration is pretty quick for routine crystallography tasks. You don't really need much in the way of hardware for XRD data processing. For image processing and movie-making in Pymol, for example, the extra cores really shine, though. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
Re: [PyMOL] Spheres for metal ions
Gary Hunter wrote: I am displaying pdb files of metalloenzymes, and like to show the metal ions as spheres. I select the metal and use showspheres Fine Somehow recently I must have done something to reset the vdw radius of manganese (MN in the pdb), as Mn atoms now display as small spheres (a little larger than solvent as nb_spheres). They were fine originally (!) and other metal atoms display at correct sizes (much bigger than my Mn). What could I have done? A global edit of sphere_scale etc. simply changes all. I reset the settingedit_all using the dialog as a check too. I can use: Alter name MN, vdw=vdw*2 Rebuild Or whatever, but I have to do it for each pdb file I read in now (if it has a Mn atom). Could I have messed with the vdw value in some way? Is there a way to actually check the values being used for vdw radii? Thanks Gary Prof. Gary J. Hunter, Department of Physiology and Biochemistry, University of Malta, Msida, MSD 06, Malta. phone: +356 2340 2917 phone: +356 21316655 (secretary), Fax: +356 21310577 Gary, You will normally have to manually adjust the ionic radius of metal ions to correctly render them. For starters, PDB files are not always good at distinguishing between atoms and ions; second, there is no single ionic radius for metal ions, as their effective radius depends on coordination number. (For example, zinc has different ionic radii for 4- and 5-coordinate compounds. A simple way to adjust radii globally by element is: alter elem zn, vdw=0.74 rebuild (This would set zinc in a protein structure to 0.74A, the appropriate value for a four-coordinate metal environment.) There are many databases out there for obtaining ionic radii. For example, see http://abulafia.mt.ic.ac.uk/shannon/ . Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
Re: [PyMOL] COVER image
Try the command png filename.png, 1200, 1600, -1, 1 to create an output image 1200 pixels wide by 1600 pixels tall, raytraced. To disable raytracing, change the last argument to zero. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu Vincent Chaptal wrote: Hello, I am trying to make a picture for a cover and I am wondering how to make a vertical image. (Pymol creates horizontal images, and journal covers are vertical) Is there a way to creates those vertical images other than turning the image 90 degrees with the 'turn z, 90' command? thanks vincent -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer. -- -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer. -- - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] The A B Cs of Pymol movies
I kind of like using Slerpy (found on the Pymol Wiki) to assemble highly controlled movies of static structures. The resulting PNG frames can be assembled into an animated GIF using ImageMagick, and if the GIFs are too big (they are lousy in Powerpoint) they can be converted to smaller more efficient AVIs using Fast Movie Processor 1.41. Animating changes between two alternative structures/conformations is a little bit trickier to do well. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu Thomas S. Leyh, Ph. D. wrote: Ok, Lots of seminars comming up, and I'd love to build cool movies into them. What is the best path to learning how to do this? There is a lot of fragmented information, but is there a manual, or web-site that provides an overview of the steps, and, ideally, then leads to specifics of how enact them. Simple things like rotating and zooming, and building that into a PowerPoint presentation would be a big help. Thanks, Tom - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Doubts regarding command line argument in pymol
bg_color white should do it. Nagarajan wrote: Hello all, I am having some doubts in command line argument in pymol. Can anyone tell me the command to change the background to white using command line..! I can use it in a movie script. Thanking you Nagarajan.P - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
