[PyMOL] Quick PyMOLWiki Update
Greetings PyMOLers, Traffic on the PyMOLWiki continues to grow. It serves far over 100k page views/month. In 2015 we got traffic from almost every country on the planet. Very cool. While operating well, the site, schemas, and plugins were outdated. So, I went through and upgraded everything (and reinstalled a few previously omitted plugins). Because of the scope of the changes, something may go wrong. If it does, please let me know. Also, curiously, today my provider let me know that the PyMOLWiki was being DDoS'd. I can imagine more productive use of one's time. If you encounter issues, please let me know. Happy New Year! I hope everyone enjoyed their holiday(s). Cheers, -- Jason -- ___ 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] PyMOLWiki: Quick Update
Greetings Shane, et. al., The issue with the database connection should be fixed permanently now. Search should also be consistently better. I've independently owned and run the wiki for almost a decade now. It's heading toward 22 million page views. Anyhow, it's now on good hardware (SSD, lots of RAM, and a nice network) and should be stable. Let me know if not. Cheers, -- Jason On Sun, Oct 18, 2015 at 6:35 PM Shane Caldwell <shane.caldwel...@gmail.com> wrote: > Hi Jason, pymol-users list, > > The pymolwiki seems to be down and has been for a few days now. It looks > like the server's down? > > Any page returns: > > (Can't contact the database server: Can't connect to local MySQL server > through socket '/var/run/mysqld/mysqld.sock' (111) (localhost)) > > Is there a mirror anywhere that can be used? > > Shane Caldwell > McGill University > > On Wed, Sep 9, 2015 at 1:02 AM, Jason Vertrees <jason.vertr...@gmail.com> > wrote: > >> Greetings, >> >> It's been a while, I hope this message finds everyone well. >> >> I'm writing to briefly let you know that I recently moved, upgraded, and >> reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast >> and more useful. Feel free to report any bugs. >> >> Back to the startup-life. >> >> Cheers, >> >> -- Jason >> >> >> -- >> Monitor Your Dynamic Infrastructure at Any Scale With Datadog! >> Get real-time metrics from all of your servers, apps and tools >> in one place. >> SourceForge users - Click here to start your Free Trial of Datadog now! >> http://pubads.g.doubleclick.net/gampad/clk?id=241902991=/4140 >> ___ >> 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] PyMOLWiki: Quick Update
Shane, Try now. Cheers On Sun, Oct 18, 2015, 6:35 PM Shane Caldwell <shane.caldwel...@gmail.com> wrote: > Hi Jason, pymol-users list, > > The pymolwiki seems to be down and has been for a few days now. It looks > like the server's down? > > Any page returns: > > (Can't contact the database server: Can't connect to local MySQL server > through socket '/var/run/mysqld/mysqld.sock' (111) (localhost)) > > Is there a mirror anywhere that can be used? > > Shane Caldwell > McGill University > > On Wed, Sep 9, 2015 at 1:02 AM, Jason Vertrees <jason.vertr...@gmail.com> > wrote: > >> Greetings, >> >> It's been a while, I hope this message finds everyone well. >> >> I'm writing to briefly let you know that I recently moved, upgraded, and >> reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast >> and more useful. Feel free to report any bugs. >> >> Back to the startup-life. >> >> Cheers, >> >> -- Jason >> >> >> -- >> Monitor Your Dynamic Infrastructure at Any Scale With Datadog! >> Get real-time metrics from all of your servers, apps and tools >> in one place. >> SourceForge users - Click here to start your Free Trial of Datadog now! >> http://pubads.g.doubleclick.net/gampad/clk?id=241902991=/4140 >> ___ >> 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
[PyMOL] PyMOLWiki Update
Greetings, It is my pleasure to let you know that Microlytic http://www.microlytic.com/, a company that makes tools for crystallographers, has graciously offered to host the PyMOLWiki. The wiki has been successfully transferred and is serving. (The search and the port : problems have been fixed. Please let me know if you find any other problems.) Please join me in thanking Microlytic http://Melanie Adams-Cioaba m...@microlytic.com for helping serve the PyMOL community. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com (o) +1 (603) 374-7120 -- 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
Re: [PyMOL] PyMOLWiki Update
Hi Suzanne, Everything should look and act exactly like it has in the past, including the address. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com (o) +1 (603) 374-7120 On Fri, Jun 20, 2014 at 10:18 AM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: Great! Thank you Microlytic! I assume that the PyMol wiki site will still have the same web address? -- *From:* Jason Vertrees [jason.vertr...@gmail.com] *Sent:* Friday, June 20, 2014 8:00 AM *To:* pymol-users *Cc:* Melanie Adams-Cioaba *Subject:* [PyMOL] PyMOLWiki Update Greetings, It is my pleasure to let you know that Microlytic https://urldefense.proofpoint.com/v1/url?u=http://www.microlytic.com/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0As=c5f009784fbe8b4462388f99a44f3232d828141afea37db017b8d2ba026b9f3d, a company that makes tools for crystallographers, has graciously offered to host the PyMOLWiki. The wiki has been successfully transferred and is serving. (The search and the port : problems have been fixed. Please let me know if you find any other problems.) Please join me in thanking Microlytic https://urldefense.proofpoint.com/v1/url?u=http://Melanie%2520Adams-Cioaba%2520%26lt%3Bmac%40microlytic.com%26gt%3Bk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0As=b2e04adca315e082abf51a6d98450782b86b9d5347605cd10510bdb863aa2146 for helping serve the PyMOL community. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com (o) +1 (603) 374-7120 -- 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
[PyMOL] Farewell
Greetings PyMOLers and CCP4ers worldwide, It has been my great pleasure to serve the PyMOL community both in a volunteer and professional capacity for the past decade. I have recently been given an offer I can't refusehttp://www.linkedin.com/in/jasonvertrees/—to follow one of my dreams—helping lead technology and science at a new startuphttp://www.realmassive.com. March 30th marked my last day at Schrödinger and supporting PyMOL. Because of my great fondness for PyMOL and its community, I will continue to operate the PyMOLWiki until I find it a suitable home. I started the PyMOLWiki in 2005 and since then it's been visited over 15,289,590 times! (If you would like to sponsor or host the wiki feel free to email me.) Now I can't imagine the PyMOL community without it. Last, I am truly humbled to have followed in the footsteps of Warren DeLano. He was an amazing man whose ideas and actions have touched the lives of millions, whether they know it or not. He is missed. It's been great fun. I wish you all the best. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com (o) +1 (603) 374-7120-- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ 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] forward and backward keyboard shortcuts
Thomas, Right and left arrow keys. Cheers, Jason On Tuesday, March 4, 2014, Thomas Evangelidis teva...@gmail.com wrote: Hi, Is there any keyboard shortcut to move to the next or the previous state of an object, namely something equivalent to forward and backward commands? -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.grjavascript:_e(%7B%7D,'cvml','tev...@pharm.uoa.gr'); teva...@gmail.comjavascript:_e(%7B%7D,'cvml','teva...@gmail.com'); website: thomasevangelidishomepagehttps://sites.google.com/site/thomasevangelidishomepage/ -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/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] RNA stick depiction with filled-out rings
Hi Claus, Maybe this: fetch 1rna, async=0 as sticks show cartoon set cartoon_side_chain_helper, 1 set cartoon_ring_mode, 1 Cheers, -- Jason On Mon, Feb 10, 2014 at 2:03 PM, Kuhn, Claus-Dieter k...@cshl.edu wrote: Hi Pymol users, I am trying to depict RNA as sticks, however with filled-out rings (bases and ribose). I have been going about doing this by combining cartoon view for the filled-out bases, using set_cartoon_radius=0 and stick view for the backbone. When doing this I am always left with a fine line of cartoon_tube, which I would love to be invisible. How can I make this line invisible? Thanks a lot. Claus -- Androi apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/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] arbitrary distance label for atom pair
Richard, The PyMOL team was just discussing this a few days back. Sadly, there is no way to do this using standard labels. If you have Incentive PyMOL v1.7 you can use the new callout command (http://pymol.org/dsc/dokuwiki/doku.php?id=command:callout). Otherwise you can use the pseudoatom (http://www.pymolwiki.org/index.php/Pseudoatom) as a label: # create a single ala frag ala # create a labeled distance dist 2/N, 2/O # hide the labels hide labels # create a new label at the center of the selection pseudoatom new_label, (2/N or 2/O), label=Some arbitrary label here: \316\261 orient Cheers, -- Jason On Tue, Feb 4, 2014 at 10:07 AM, Richard Smith re...@cam.ac.uk wrote: Hi, Is there an easy way to change the label on a distance object to some arbitrary string? I would like a line connecting two atoms with an arbitrary label at the midpoint between the two atoms. for example: #make atom pair selection distance d, (id 3651, id 3691) # actual distance = 2.00 #replace 2.00 with 100% # or any other string label d, 100% Thanks. -- --- Regards Richard Smith Research Associate Department of Zoology Smith Research Group University of Cambridge Downing Street Cambridge CB2 3EJ Tel.: +44 (0)1223 330933 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/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 on Coursera
Greetings, I am happy to report that PyMOL will be used in a structural biolnformatics lab of an upcoming Coursera course, Bioinformatic Methods 2, taught by Nicholas Provart of the University of Toronto. The enrollment for these courses can typically be in the tens of thousands or more. If you would like to learn more about this free online course visit https://www.coursera.org/course/bioinfomethods2. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/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] List residues functionality ?
Carsten, What about http://www.pymolwiki.org/index.php/List_Selection and http://www.pymolwiki.org/index.php/List_Selection2? I also made a similar script for retrieving object names: http://www.pymolwiki.org/index.php/GetNamesInSel. Cheers, -- Jason On Fri, Jan 31, 2014 at 10:30 AM, Schubert, Carsten [JRDUS] cschu...@its.jnj.com wrote: Hi All, probably a question for the developers, but may not hurt to ask publicly: Is there a functionality in Pymol to list the residues in a given selection? I am looking for the equivalent to the get_chains() function. I have scripted something up, but the code is not 100% clean and not flexible enough. For large molecules the performance is not great either. start script def list_resi(obj=): DESCRIPTION list_resi prints and returns the unique residue IDs from the input object. The object must be present in the object list on the GUI. Selections are currently not implemented. Chain or Segments are also not taken into account USAGE list_resi obj EXAMPLES list_resi my_prot l = list_resi(my_prot) if ( obj == ): obj=(all) ol = cmd.get_object_list() if (obj in ol): pass else: print Error: Object (%s) not found % obj return stored.resi_list = [] cmd.iterate(obj,stored.resi_list.append(int(resi))) stored.resi_list=list(set(stored.resi_list)) # make list unique stored.resi_list.sort() for i in range(0,len(stored.resi_list)): print %s, % stored.resi_list[i], if ((i+1) % 10 == 0): print return stored.resi_list # End Script Thanks for any input Carsten -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/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] Write map from list of coordinates.
Hi Esben, I have a list of coordinates on a regular grid with associated floating point values from a calculation that I want to visualise in PyMOL. Is it nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently load it, or can it be loaded directly into a map object via some fancy python code? It depends on how you want to visualize the data. If dots/points or other discrete representations are okay then you can use a XYZ or a modified structure file. If you want the benefit of a field (volume, gradient, isosurface) then I suggest the map. If you already have the data in a well-formatted brick, check out the asCCP4 function in http://www.pymolwiki.org/index.php/Tiff2ccp4. That writes the CCP4 header and data (of a TIFF file, but you can modify that for your needs). If you want, send me a copy of your data. Or, I also have a very poorly written script that will convert raw volumes of data to CCP4 maps, similar to the aforementioned script. Email me personally and I can send you a copy if you prefer (but it's really ugly code). Cheers, -- Jason On Wed, Jan 29, 2014 at 8:02 AM, Esben Jannik Bjerrum esbenjan...@rocketmail.com wrote: Hi All-knowing Pymol'ers. I wonder if anyone had a couple of tips/ pointers / script snippets. I have a list of coordinates on a regular grid with associated floating point values from a calculation that I want to visualise in PyMOL. Is it nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently load it, or can it be loaded directly into a map object via some fancy python code? Best Regards Esben Jannik Bjerrum -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/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] Error while starting Pymol 1.7
Hi Roy and Carsten, Adding new features, like volume rendering, often requires using new technology. We added geometry shaders to PyMOL v1.7 to support rendering the new labels/callouts. Your video card does not appear to support geometry shaders. Many users remedy this problem by updating their graphics drivers. But, sometimes this doesn't help. PyMOL works best with a dedicated graphics card. Integrated rendering systems that share system memory, which are often found on a laptops, are not sufficient for optimal PyMOL rendering. If PyMOL cannot compile or execute a shader then PyMOL disables GLSL-based rendering and falls back to the old-style fixed pipeline. In that case PyMOL complains but should still work, offering basic functionality. This way we can offer basic rendering for old or weak hardware while adding new features for better graphics cards. Last, we do not code only for NVidia cards. We stick to the OpenGL specification. Thus those systems that run PyMOL better have video cards and drivers that more thoroughly implement the OpenGL specification. Cheers, -- Jason On Mon, Jan 27, 2014 at 6:44 AM, Roy Eylenstein roy.eylenst...@morphosys.com wrote: Dear all, I see following error message when starting pymol 1.7 incentive on Win 7 enterprise SP1 32 bit (i3 M370) This Executable Build integrates and extends Open-Source PyMOL 1.7.0.1. Detected OpenGL version 2.0 or greater. Shaders available. CShaderPrg_New-Error: geometry shader compilation failed name='connector'; log follows. infoLog=ERROR: 0:2: '' : extension 'GL_EXT_geometry_shader4' is not supported ERROR: 0:3: '' : extension 'GL_EXT_gpu_shader4' is not supported ERROR: 0:5: 'vec3' : syntax error parse error Any suggestions? Best, Roy MorphoSys AG - Lena-Christ-Str. 48 - 82152 Martinsried/Planegg - Germany; Handelsregister/Commercial Register: Amtsgericht München HRB 121023; Vorstand/Management Board: Dr. Simon Moroney (Vorstandsvorsitzender/CEO), Jens Holstein (Finanzvorstand/CFO), Dr. Arndt Schottelius (Entwicklungsvorstand/CDO), Dr. Marlies Sproll (Forschungsvorstand/CSO); Aufsichtsrat/Supervisory Board: Dr. Gerald Möller (Vorsitzender/Chairman) This message may contain confidential and/or privileged information. If you are not the addressee or authorized to receive this for the addressee, you must not use, copy, disclose or take any action based on this message or any information herein. If you have received this message in error, please advise the sender immediately by reply e-mail and delete this message. Thank you for your cooperation. Diese E-Mail kann vertrauliche und/oder rechtlich geschuetzte Informationen enthalten. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtuemlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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] Font problem
Justin, Yes, we put quite a bit of effort into improving the font rendering. It's still not perfect, but should be improved over the pre-release versions. Please let me know where you still have issues. (Just send me a PSE file as an example.) Cheers, -- Jason On Tue, Jan 21, 2014 at 5:27 AM, Justin Lecher j.lec...@fz-juelich.dewrote: On 22/11/13 17:44, Jason Vertrees wrote: Hi Justin, We'll fix that, too. Cheers, -- Jason Hi Jason, did you find time to look into that? Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 v1.7 Released
Michael, Nice catch—we'll fix it. Thanks for letting us know. Cheers, -- Jason On Mon, Jan 20, 2014 at 9:11 AM, Michael Banck mba...@gmx.net wrote: Hi, On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote: We are happy to announce the release of PyMOL v1.7.0.0! Congrats! One thing though: the open-source splash image has not been updated for 1.7 and still says 1.6.x. Michael -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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, number and label the helices
Gefei, Please read about labels (http://www.pymolwiki.org/index.php/Label; and http://www.pymolwiki.org/index.php/Category:Labeling) and pseudoatoms ( http://www.pymolwiki.org/index.php/Pseudoatom). These should help you label what you need to. Cheers, -- Jason On Mon, Jan 20, 2014 at 9:57 AM, Gefei Chen cgf-2...@hotmail.com wrote: Hi guys, I am now preparing some proteins structure figures, and I think Pymol is a good program. But now something happened to me, my protein just has 5 helices, and I want to number and label the helices as H1, H2 …and H5 in the figure with using Pymol directly (not photoshop), but I am sorry I have no idea for finishing it, however I have read the guide of Pymol. could anyone tell me something about how to number and label the helices? That will be very helpful, and thank you very much! Best wishes, Gefei -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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] mutagenesis wizard data file loading
Michael, I think you're right. We'll make and push the changes. Cheers, -- Jason On Mon, Jan 20, 2014 at 10:40 AM, Michael Banck mba...@gmx.net wrote: Hi, I noticed that the mutagenesis wizard uses PYMOL_PATH/data to locate the chempy sidechains, however, PYMOL_DATA would be more appropriate if the data is not installed alongside the pymol modules. The attached patch fixes this. Michael -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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] combining multiple objects into one multistate object
Jed, You are correct in that you should be using the create command: # creates new_obj from old_obj1 by copying old_obj1 # in state 1 to new_obj in state 1 create new_obj, old_obj1, 1, 1 # creates new_obj from old_obj2 by copying old_obj2 # in state 1 to new_obj in state 2 create new_obj, old_obj2, 1, 2 # creates new_obj from old_obj3 by copying old_obj3 # in state 1 to new_obj in state 3 create new_obj, old_obj3, 1, 3 If you have any empty session, this will automate the process: python for x in cmd.get_names(): cmd.create(combined_models, x, 1, -1) python end Cheers, -- Jason On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.edu wrote: I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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] combining multiple objects into one multistate object
Jed, Yes, the create command should more intelligently handle the wildcard. In fact, I started out trying the same thing you did. I'll add this as a feature request. Cheers, -- Jason On Thu, Jan 16, 2014 at 10:06 AM, Jed Goldstone jgoldst...@whoi.edu wrote: Thanks! That works. I kept trying to avoid writing a script, figuring that it should just be an option in 'create'. That is, if the selection old_obj has a wild card, then create new_obj, old_obj*,1,-1 should work. Clearly not; could this be a future feature? Jed On 1/16/2014 10:56 AM, Jason Vertrees wrote: Jed, You are correct in that you should be using the create command: # creates new_obj from old_obj1 by copying old_obj1 # in state 1 to new_obj in state 1 create new_obj, old_obj1, 1, 1 # creates new_obj from old_obj2 by copying old_obj2 # in state 1 to new_obj in state 2 create new_obj, old_obj2, 1, 2 # creates new_obj from old_obj3 by copying old_obj3 # in state 1 to new_obj in state 3 create new_obj, old_obj3, 1, 3 If you have any empty session, this will automate the process: python for x in cmd.get_names(): cmd.create(combined_models, x, 1, -1) python end Cheers, -- Jason On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.eduwrote: I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 v1.7 Released
Greetings, We are happy to announce the release of PyMOL v1.7.0.0! Official PyMOL sponsors can download ready-to-use installers from http://pymol.org/dsc/ip . The open-source code has been pushed to sourceforge svn (revision 4060) and a downloadable bz2 source file is also available from http://sf.net/p/pymol/. A few improvements include: Incentive PyMOL (for licensed users) * Improved labels, with connectors, backgrounds, outlines, and multiline text * Callouts for general labeling * 675 documented settings in the Settings Edit All GUI * New Find Wizard (CTRL-F) for locating objects in the object menu panel * ...and more Open Source and Incentive PyMOL * Added the focal_blur command * Added the get_renderer command to return information about the graphics renderer * Fetch command now takes SID and CID codes for PubChem * New selection keywords: metals, backbone, and sidechain * Access to settings and properties from the iterate/alter commands * Improved the PDB Loader GUI * Lots of Bugs Fixes AxPyMOL (for licensed users): * Built as a PowerPoint Add In * Option to embed data into the PowerPoint file * Supports PowerPoint PPTX files * Added support for presenting Maestro (.mae and .maegz) files * Added support for Windows 8, MS Office 2010 and 2013 (32- and 64-bit) * Support for shader-based rendering We encourage PyMOL sponsors to check out the internal documentation: * -- http://pymol.org/dsc/dokuwiki/doku.php?id=media:new17 We welcome any feedback and bug reports. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 and Oculus Rift
Hi Matthew, I had a chance to play with the Oculus Rift, but have not added it to PyMOL as an input device. While definitely a cool device, its integration would have to be well-thought out: with PyMOL you look at a given point and rotate data around that point whereas with the Oculus Rift, the viewer's head is the center of rotation. Cheers, -- Jason On Fri, Jan 10, 2014 at 1:45 PM, Matthew Baumgartner mp...@pitt.edu wrote: Hi, Has anyone tried to get pymol working with the Oculus Rift? I just got my hands on one and I think it would be awesome to use it with pymol? Thanks, Matthew Baumgartner -- -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/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] Selection algebra issue
Hi Katherine, PyMOL can do what you want. I've done this exact task before. Here's the idea. If you have a PDB with multiple ligands and you use, select allLigands, organic and myProtein you create the selection allLigands which contains all the ligand atoms in myProtein. What you need to do is extract each ligand, molecule by molecule, from the allLigands selection using selection algebra until myLigands is empty. It's done like this: # create a selection containing the atoms of all ligands select allLigands, organic and myProtein # create a selection to use later as we iterate across # all ligands, this will hold individual ligands we extract # from allLigands select current_ligand, none # enter a Python block so we can use Python while-loop # and other Python syntax python # loop until allLigands is not empty while cmd.count_atoms(myLigands) 0: # copy the first ligand selection, by molecule, into # the, current_ligand cmd.select(current_ligand, bm. first allLigands) # do something with current_ligand, like finding all ligands # without waters nearby if cmd.count_atoms(solvent within 5 of current_ligand) == 0: print This is an interesting ligand. # now remove current_ligand from allLigands # and loop again cmd.select(allLigands, allLigands and not current_ligand) python end Good luck! Cheers, -- Jason On Fri, Dec 13, 2013 at 4:58 PM, Katherine Sippel katherine.sip...@gmail.com wrote: Hi Carsten, Thanks for the help. I've tried variants of that selection and it works great if there is only one ligand. Unfortunately it breaks down when there are multiple ligands and they don't all fit the criteria. I'm surveying almost half the PDB so these are all different proteins with different binding sites and ligands. I was hoping for a way to get pymol to recognize each individual ligand automatically by grouping common resids within the non-solvent hetatm selection. Using the %s %(resi) seems to require an explicit input. I might be able to extract an explicit chain/resi designation for each file from the het portion of the pdb header, though I'm not sure how to automate this. I suppose it's back to the script repository for me. Cheers, Katherine On Fri, Dec 13, 2013 at 2:50 PM, Schubert, Carsten [JRDUS] cschu...@its.jnj.com wrote: Katherine, not sure if that is what you are looking for but you can select for non-polymer residues with: select lig, prot and organic That will select any non polymer (protein and R(D)NA) residues present in the pdb. You then would need to break the selection further into the individual constituents, by either chain Id and resid. Hope this helps a bit. Carsten From: Katherine Sippel [mailto:katherine.sip...@gmail.com] Sent: Friday, December 13, 2013 10:28 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Selection algebra issue Hi all, I'm trying to write a script to data mine the pdb. I'm want to look at the ligands in a pdb file and fish out those that meet a certain criteria. I've got a script that can look at the ligands all at once but I need to assess each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to define them individually. I've tried variations on %s' % (resi) and bymolec but I can't seem to figure out how to get them parsed separately without specifying a number. I've also tried using index to create a tuples list and iterating from that but I keep hitting the same issue. I've attached a couple of the attempted scripts so you can laugh at my google derived python skills. I've been trying to figure this out for a week now and I'm completely stumped. If anyone could nudge me in the right direction, even if it's some Pymolwiki article I missed, I would appreciate it immensely. Thanks for your time, Katherine -- Nil illegitimo carborundum - Didactylos -- Nil illegitimo carborundum - Didactylos -- 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear
Re: [PyMOL] what is an object colored ?
Jon, You can also iterate over a selection and show the color index for each color iterate *, color You can then color by those indices, eg: color 26 Cheers, -- Jason On Mon, Nov 25, 2013 at 5:42 AM, Jonathan Grimes jonat...@strubi.ox.ac.ukwrote: dear all, i am having implementing these instructions. i would like to work out what color an object is…… how is this defined ….. s[names][1][5][0][1] equals your object name. if I have an object called A1…i am unsure how to make A1 equal to s[names][1][5][0][1] many thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 On 12 Dec 2012, at 17:24, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Jon, ive been given a pse file.and i am trying to work out what color an object is.. i used the command get cartoon_color, pT_A and got back get: cartoon_color = default in object pT_A You're right, that's not very helpful. This will get you the answer, but it's not very straightforward: s = cmd.get_session() print cmd.get_color_tuple(s[names][1][5][0][2]) To make sure you have right object ensure that, s[names][1][5][0][1] equals your object name. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
Hi, Is there any chance you can send me your input file(s)? Also, please let me know what computer, video card, and architecture (32-bit/64-bit) you're running on. Cheers, -- Jason On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский croov...@gmail.comwrote: Hello I run PyMol 1.6.0 on windows 7 and I get this error: ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282 or ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282 over and over again. Is there any way to get rid of that? That's really annoying. crooveck -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
Hi Pawel, I suggest making sure that your video drivers are up to date at all times when using software like PyMOL. Mobile video cards notoriously badly implement the OpenGL spec. If that's a bug in our part, we'll try to track it down. Cheers, -- Jason On Sun, Nov 24, 2013 at 3:42 PM, Павел Томашевский croov...@gmail.comwrote: 2013/11/24 Jason Vertrees jason.vertr...@schrodinger.com: Hi, Hi Jason Is there any chance you can send me your input file(s)? Also, please let me know what computer, video card, and architecture (32-bit/64-bit) you're running on. So basically this problem occurs every time I start pymol, even without loading any input files. My computer is Dell Latitude E6400, running Windows 7 64-bits, I have Nvidia Quadro NVS160M. I've installed newest drivers a few days ago, but the problem still exists. If it matters... I've obtained PyMol executables (already compiled) from http://www.lfd.uci.edu/~gohlke/pythonlibs/3msnvi49/pymol-1.6.0.0.win-amd64-py2.7.exe . Executable comes with integrated Python 2.7 distribution... Cheers, -- Jason Cheers Pawel On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский croov...@gmail.com wrote: Hello I run PyMol 1.6.0 on windows 7 and I get this error: ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282 or ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282 over and over again. Is there any way to get rid of that? That's really annoying. crooveck -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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] Font problem
Hi Justin, We'll fix that, too. Cheers, -- Jason On Fri, Nov 22, 2013 at 1:24 AM, Justin Lecher j.lec...@fz-juelich.dewrote: On 22/11/13 01:02, Thomas Holder wrote: Hi, this is fixed now in the sourceforge SVN repository. Cheers, Thomas Thanks for working quickly on it, but it isn't fixed here. There some things I observe, The font geometry changes according to the window geometry. That means a tall thin window creates tall, stretched fonts. I would say, that font geometry should be independent from the window size. Probably coming from the same source in the code, the fonts get ugly when maximizing a window on a 27'' screen. This scaling problem also depends on use_shaders. I am using rev. 4052 Regards, Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 sas
Neshat, Warren wrote the surfacing algorithm years ago. A little more discussion on the algorithm can be found here ( http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07124.html) and here (http://www.pymolwiki.org/index.php/Get_Area). Cheers, -- Jason On Tue, Nov 12, 2013 at 2:17 AM, neshat haq neshat...@gmail.com wrote: Hi, I could not find the the algorithm by which pymol calculates the solvent ASA. What I understood is that pymol adds the vdw radii of atom and probe, makes the sphere around the center of selected atoms, puts some dots and according to the density of dots it calculates the SASA. or it simply uses the Richard Lee algorithm of rolling water. Please clarify my doubts. -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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] Font problem
Justin, You're right, they are ugly! We're fixing that ASAP. Thanks for bringing this up. Cheers, -- Jason On Thu, Nov 21, 2013 at 8:10 AM, Justin Lecher j.lec...@fz-juelich.dewrote: Hi, label fonts look ugly here with use_shaders=1. When switching on use_display_lists=1 it looks good again. But the two options are exclusive so I get a performance penalty for the gain of good looking fonts. After ray tracing the fonts look great in both cases. Is there a way to improve the font rendering during shader activated mode? thanks Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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] UCSD pymol workshop
Hi Spencer, We're happy to help. Please email me offline and I'll see how we can assist. Cheers, -- Jason On Wed, Nov 20, 2013 at 5:30 PM, Spencer Bliven sbli...@ucsd.edu wrote: We've been discussing putting together a PyMol workshop for the UCSD undergrad bioinformatics club (http://ubic.ucsd.edu/). I wanted to ping this list and see if anyone in the San Diego area would be interested, either as attendants or as an instructor or assistant. I would like hearing if anyone has resources they found particularly useful when learning to use pymol - tutorials, slides, etc. Thanks! Spencer -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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] How to make outlines to spheres drawn in PyMOL ?
Anasuya, set ray_trace_mode, 1 Cheers, -- Jason On Tue, Nov 19, 2013 at 12:24 AM, Anasuya Dighe anas...@mbu.iisc.ernet.in wrote: Dear users, I was interested in knowing if there is an option or setting in PyMOL which is able to make an outline to spheres. I am aware of the show spheres command and have used it extensively to show C-alpha atoms of amino acids as spheres. I am curious to know how I could make an outline to the C-alpha atoms in a particular selection. Also, once the outline is made, how might I be able to change the color of such an outline ? Please let me know. Thanks, Anasuya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/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] apply spectrum per MODEL in PyMOL script
Hi Jerome, fetch 1nmr, discrete=1, async=0 as ribbon set all_states for x in range(cmd.count_states()): cmd.color(str(x), state %s % x) You can substitute the spectrum command for the color command. Cheers, --- Jason On Sat, Nov 9, 2013 at 8:54 PM, Jerome BENOIT g62993...@rezozer.net wrote: Hello List, is there a way in PML script to apply a specific spectrum to each MODEL (as define in PDB data file) ? Thanks in advance, Jerome -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default values in pymol?
Hi Neshatul, # print out the vdw values used for a given selection iterate my_selection, vdw Use alter to change the values: alter my_selection, vdw=vdw+2.0 Cheers, --Jason On Sat, Nov 9, 2013 at 4:17 PM, neshat haq neshat...@gmail.com wrote: Can anyone tell where can I get the default values of van der wall radii (or other radii) used in pymol, for atoms and combinations of atoms, like C, N, O, C=O, CH3, ..etc -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] [WAS: polygonal ring] cyclic peptide
Hi Jerome, PyMOL doesn't yet handle cyclic peptides. It's an open case we hope to resolve soon. Cheers, -- Jason On Tue, Nov 5, 2013 at 1:47 AM, Jerome BENOIT g62993...@rezozer.net wrote: Hello Again, let rephrase my question: does PyMOL have support for cyclic peptide (ex. 2NS4) ? Thanks, Jerome On 29/10/13 17:37, Jerome BENOIT wrote: Hello List, So far I use PyMOL to visualize polygonal chain through an expurged PDB data file when the chain is not ring. Now I would like to visualize chain rings: what is the best way to make PyMOL understand that the two end points coincide ? Thanks in advance, Jerome -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] [WAS: polygonal ring] cyclic peptide
Jerome, One has already been filed internally. If you'd like, feel free to open on on the open-source tracker (https://sourceforge.net/p/pymol/feature-requests/). Cheers, -- Jason On Tue, Nov 5, 2013 at 9:54 AM, Jerome BENOIT g62993...@rezozer.net wrote: Hello, thanks for the reply. May a ticket be filled ? Jerome On 05/11/13 15:34, Jason Vertrees wrote: Hi Jerome, PyMOL doesn't yet handle cyclic peptides. It's an open case we hope to resolve soon. Cheers, -- Jason On Tue, Nov 5, 2013 at 1:47 AM, Jerome BENOIT g62993...@rezozer.net wrote: Hello Again, let rephrase my question: does PyMOL have support for cyclic peptide (ex. 2NS4) ? Thanks, Jerome On 29/10/13 17:37, Jerome BENOIT wrote: Hello List, So far I use PyMOL to visualize polygonal chain through an expurged PDB data file when the chain is not ring. Now I would like to visualize chain rings: what is the best way to make PyMOL understand that the two end points coincide ? Thanks in advance, Jerome -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] cylindrical helices
Andreas, That's an interesting find. PyMOL is clearly being fooled by the secondary structure assignment. I don't think it's PyMOL's responsibility to address egregious cases like this—rare and non-standard. You can run 'dss' to update the secondary structure to something more reasonable or you can use the 'alter' command to update the secondary structure assignments. That should improve the result. Cheers, -- Jason On Fri, Nov 1, 2013 at 7:33 AM, Andreas Förster docandr...@gmail.comwrote: Dear all, I've just been baffled for a while with a pdb that showed a strange behavior upon changing the representation from cylindrical cartoon helices to normal cartoon helices. It seemed to me that helices were disappearing. A picture of the effect is here: http://www.msf.bio.ic.ac.uk/images/helices.png The arrows show pairs of normal helices merged into single short cylindrical helices. At some point, I realized the problem was the definition of pairs of helices as one continuous secondary-structure element (encircled). Running dss on the file fixed everything. I'm left wondering whether PyMOL should realize it's being fooled by the secondary structure predictions in egregious cases like this. I looked hard at the structure with cylindrical helices and started to interpret differences to a homologous structure, which seemed to have additional helices, and in perpendicular orientations. Best regards. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/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] Is object enabled or disabled?
Hi Chris, if objName in cmd.get_names(enabled_only=1): print objName is enabled Cheers, -- Jason On Tue, Oct 29, 2013 at 5:50 AM, Christoffer Norn ch.n...@gmail.com wrote: Hi All, How can I, from the command line, get information on whether a object is enabled or disabled? I need this to flip through thousands of designed proteins — and with this many proteins, mouse-clicking to enable/disable them becomes a bit cumbersome. Thanks, Chris -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/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] neutral aminoacids
Osvaldo, To make PyMOL pick fragments from another location just edit the path at the top of pymol/modules/chempy/fragments/__init__.py. The fab command is in pymol/modules/pymol/editor.py. Cheers, -- Jason On Thu, Oct 10, 2013 at 11:38 PM, Osvaldo Martin aloctavo...@gmail.com wrote: BTW, there is an easy option to make cmd.fab() to pick the fragments from an alternative location? (just to avoid modifying the original fragments files) thanks, Osvaldo. On Fri, Oct 11, 2013 at 12:32 AM, Osvaldo Martin aloctavo...@gmail.com wrote: Ok, I will try editing those files. Cheers, Osvaldo. On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Osvaldo, This isn't built in yet. But, if you need to do that, you can edit the Python picked files found here: pymol/data/chempy/fragments Cheers -- Jason On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin aloctavo...@gmail.com wrote: I am using the comand cmd.fab() to create small peptides. There is an easy option to add neutral aminoacids? The default behaviour is to add charged amino acids with the charge of the free amino acid in solution at pH = 7 i.e. Lys and Arg protonated and Glu, Asp and His unprotonated. Thanks in advance. -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/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] selection residues with an exact b-factor value
Hi Mike, We didn't implement the equals operator, but the less than and greater than operators are strict comparisons so you can do the following: select my_exact_b, not (b0.5 or b0.5) Cheers, -- Jason On Thu, Oct 10, 2013 at 9:34 PM, Osborne Michael michael.osbo...@umontreal.ca wrote: Hello Pymolers I think this is an easy one, but I can't seem to get this to work. I'd like to select residues with a bfactor equal to a certain value, say 0. However something like: select aa, b = 0 does not work although select aa, b 0.5 does work. Cam someone show me how to do this? Cheers Mike -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/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] neutral aminoacids
Hi Osvaldo, This isn't built in yet. But, if you need to do that, you can edit the Python picked files found here: pymol/data/chempy/fragments Cheers -- Jason On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin aloctavo...@gmail.com wrote: I am using the comand cmd.fab() to create small peptides. There is an easy option to add neutral aminoacids? The default behaviour is to add charged amino acids with the charge of the free amino acid in solution at pH = 7 i.e. Lys and Arg protonated and Glu, Asp and His unprotonated. Thanks in advance. -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/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] load surface
Hi Alexander, See http://www.pymolwiki.org/index.php/Wfmesh. Cheers, -- Jason On Fri, Sep 27, 2013 at 3:05 PM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, I have create a surface (vertices and faces) in some external program and am now looking for a format to convert it to so that PyMOL can natively load it. Any suggestion is much appreciated. Best Alexander -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/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] Background colors in PyMOL 1.6
Hi Nils, Thomas will soon fix the return values of the get command for color to properly contain the 0x prefixes. In the meantime, please add them yourself if this is causing lots of problems: # prepend the result with 0x x = 0x%s % (cmd.get(bg_rgb_top)) # set the color cmd.set(bg_rgb_bottom, x) Cheers, -- Jason On Fri, Sep 20, 2013 at 11:36 AM, Nils NN n...@gmx.ch wrote: Hi Jason, thanks for the reply. Your method works well for the single color background. For the gradient BG however the problem still remains: PyMOLset bg_gradient, 1 PyMOLget bg_rgb_top - this returns '4d', which seems to be the hex-value. However when I try to set the bg_rgb_top/bottom value (regardless if I use hex or rgb-list) I still get an endless output of: Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 663 ... This message keeps flooding the output shell until I close the program. I guess this is rather a bug than intended? Best, Nils Gesendet: Donnerstag, 19. September 2013 um 17:39 Uhr Von: Jason Vertrees jason.vertr...@schrodinger.com An: Nils NN n...@gmx.ch Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Betreff: Re: [PyMOL] Background colors in PyMOL 1.6 Hi Nils, We've updated how PyMOL stores colors in sessions. You can try, cmd.get_color_tuple(cmd.get(bg_rgb)) or if you need it as a list: list(cmd.get_color_tuple(cmd.get(bg_rgb))) Cheers, -- Jason On Thu, Sep 19, 2013 at 5:17 PM, Nils NN n...@gmx.ch wrote: Hello, I recently installed PyMOL 1.6 on my Debian machine. I have noticed that the description of the background colors has somehow changed. The command get bg_color returns [R,G,B] values in all previous versions, while since 1.6 it only returns values like black (which messes up some of my plugins and scripts). I'm not sure if this some kind of bug or a new way of handling colors... When I try to set the background gradient colors (set bg_rgb_top/bottom) I get an endless output of Setting-Error: type read mismatch (color) 664 - I have to kill and restart the program to get rid of the message. Same happens with my scripts using cmd... Can someone confirm these problems? Perhaps I'm doing something wrong here. Thanks in advance, Nils -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk[http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk] ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net[ PyMOL-users@lists.sourceforge.net]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users[https://lists.sourceforge.net/lists/listinfo/pymol-users] Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net[http://www.mail-archive.com/pymol-users@lists.sourceforge.net] -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com[jason.vertr...@schrodinger.com] (o) +1 (603) 374-7120 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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] Background colors in PyMOL 1.6
Hi Nils, We've updated how PyMOL stores colors in sessions. You can try, cmd.get_color_tuple(cmd.get(bg_rgb)) or if you need it as a list: list(cmd.get_color_tuple(cmd.get(bg_rgb))) Cheers, -- Jason On Thu, Sep 19, 2013 at 5:17 PM, Nils NN n...@gmx.ch wrote: Hello, I recently installed PyMOL 1.6 on my Debian machine. I have noticed that the description of the background colors has somehow changed. The command get bg_color returns [R,G,B] values in all previous versions, while since 1.6 it only returns values like black (which messes up some of my plugins and scripts). I'm not sure if this some kind of bug or a new way of handling colors... When I try to set the background gradient colors (set bg_rgb_top/bottom) I get an endless output of Setting-Error: type read mismatch (color) 664 - I have to kill and restart the program to get rid of the message. Same happens with my scripts using cmd... Can someone confirm these problems? Perhaps I'm doing something wrong here. Thanks in advance, Nils -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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] C-aplha c-alpha distances
Hi Ananya, This is easily doable in PyMOL. If you've already aligned the two structures and, let's stay they're called protein1 and protein2, then use rms_cur: rms_cur protein1 and guide, protein2 and guide If the initial and final structures are in the same object loaded from disk then you can easily copy the last state to a new object using create then use rms_cur: # extract state 20 from my_trajectory and make it state 1 # in final_copy. Here I use 20, but you use whichever # state is your final state. create final_copy, my_trajectory, 20, 1 # do the RMS calculation rms_cur initial, final_copy Cheers, -- Jason On Tue, Sep 10, 2013 at 10:21 AM, Ananya Chatterjee ananya...@yahoo.in wrote: Dear all, I have aligned two structures (one the initial structure and another one is the final structure after MD simulation) in pymol, now I want to measure the C-alpha- C-alpha distances of each residue between the initial and the final structure of the MD simulation. Is it possible to do it by pymol, if yes then how to do it. Please help me in this regard I am very new to this field. Thank u in advance, Ananya -- How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system of record for IT 2. Standardize and globalize service processes across IT 3. Implement zero-touch automation to replace manual, redundant tasks http://pubads.g.doubleclick.net/gampad/clk?id=5127iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system of record for IT 2. Standardize and globalize service processes across IT 3. Implement zero-touch automation to replace manual, redundant tasks http://pubads.g.doubleclick.net/gampad/clk?id=5127iu=/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] Alpha Channels in Pymol Movies
Hi Jordan, If ray_trace_frames is on, and ray_opaque_background is off then during the moviemaking process PyMOL uses the background color in the movie. At present, I think your only workaround is to export the PNGs with transparencies and use a professional-quality movie exporter, like Adobe Premier Pro (or similar). Cheers, -- Jason On Tue, Jul 23, 2013 at 7:23 PM, Jordan Willis jwillis0...@gmail.com wrote: Hello, I'm using MacPymol 1.5.0.4 When I save a ray traced .PNG file with set ray_opaque_background, 0 It does gives me a transparent background when I put the picture into other apps, e.g. Powerpoint. However, when I save it as a .mov file, I can see that pymol is trying for a transparent background (I can see each frame as a checkerboard), but the finished product is a solid black background that looks terrible. Has anyone encountered this problem and have a possible solution or workaround? Jordan -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/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 OpenGL ES?
Hi Paul, We have plans to create the Android port, too (and have already have the core cross compiled). But, we chose not to commit to it at that time because the Android tablet space wasn't mature enough. We hope to revisit that decision soon. Cheers, -- Jason On Wed, Jul 17, 2013 at 11:13 AM, Paul Paukstelis pauks...@umd.edu wrote: Hi Jason, I did realize there was an iPad version, but I guess I was wondering if there was perhaps something more general. For example, I'm natively running linux on a Galaxy Note 10.1, and there will likely be more linux tablets popping up. For me (and likely others now or in the future), pymol would really make it a complete mobile device. --p On 07/17/2013 12:02 PM, Jason Vertrees wrote: Hi Paul, It's been done already. See, PyMOL on the iPad (http://pymol.org/mobile). Cheers, -- Jason On Wed, Jul 17, 2013 at 10:55 AM, Paul Paukstelis pauks...@umd.edu wrote: Just out of curiosity, are there any plans to port pymol over to use OpenGL ES to bring it to more mobile devices? -- Paul Paukstelis, Ph.D Assistant Professor University of Maryland Chemistry Biochemistry Dept. Center for Biomolecular Structure Organization pauks...@umd.edu 301-405-9933 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/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 -- Paul Paukstelis, Ph.D Assistant Professor University of Maryland Chemistry Biochemistry Dept. Center for Biomolecular Structure Organization pauks...@umd.edu 301-405-9933 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/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] python module in pymol
Hi Pascal, PyMOL treats .pml and .py files differently. The cluster_count script was written as a .py file as needs to be used as such. run cluster_count.py cluster_count PO4 worked just fine when run as a Python file. Cheers, -- Jason On Tue, Jul 9, 2013 at 6:06 AM, Pascal Auffinger p.auffin...@ibmc-cnrs.unistra.fr wrote: Hi, I tried to use the cluster_count script (http://www.pymolwiki.org/index.php/Cluster_Count) in a pymol.pml file. Unfortunately I get the following message: --- PyMOLcluster_count PO4 Traceback (most recent call last): File /home/sws2/Desktop/pymol/modules/pymol/parser.py, line 464, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1 cluster_count PO4 ^ SyntaxError: invalid syntax --- (PO4) is a selection of five atoms When I use the same script as a pymol plugin, it works fine when I type in the command cluster_count PO4 Any idea ??? Thanks for helping, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr - -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/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] Trouble with mutagenesis script
Hi Dan, You're missing a slash. You have: PyMOL.exe -qc mutate.py -- digly.pdb digly A/2 ASN where you should have PyMOL.exe -qc mutate.py -- digly.pdb digly A/2/ ASN When the residue is properly selected you'll see this: Selected! Mutagenesis: 4 rotamers loaded. ExecutiveRMS: RMS =0.083 (4 to 4 atoms) Mutagenesis: 12 rotamers loaded. where the RMS will change based on your residues. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] Pymol DLP 3D
Hi Colin, Does anyone have any experience in running pymol in 3D using a DLP projector? I have an Optoma EW610ST, running from a windows seven machine using a Geforce GT620 GPU. The computer and projector are connected via HDMI but at present I am not able to configure any 3D output. GeForce cards are incapable of presenting windowed OpenGL 3D at 120 Hz. You need a Quadro card. The NVidia 3D Vision ( http://www.nvidia.com/object/3d-vision-main.html) page should have all the info you need. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] Anaglyph colours sorted (kind of)
Hi Gary,
I think you misunderstood.
First, with a good video card, use Setting Rendering Modernize for
the fastest and highest quality on screen rendering. In fact, it's
essentially as good as ray tracing but without shadows. If your
machine cannot handle this, the fallback is immediate mode rendering,
which PyMOL has been using for years. Machines with older and lower
quality video cards sometimes cannot handle this rendering technique:
they're simply incapable of using such drawing techniques.
Point 4 should now be:
4) do not use 'ray' when trying to use anaglyph stereo. This is a shame
because an anaglyph image for a slide or printout might be useful.
You have this backwards. The 'ray' command works just fine in anaglyph
mode. I've made countless 3D images using 'ray' and anaglyph mode.
Some irreversible colour changes are frustrating after working for hours on
molecular structures, and then finding anaglyph does not work. That’s why I'd
like to find a 'reset' command for the settings – edit all settings.
Initialise wipes out all my hard work (molecules, objects, selections, maps,
etc etc). Currently I just have to revert to the last saved pse file.
Since we do not have 'undo' for things like colors you have to save
keep saving your session files so you don't lose any color changes.
Any idea why using modern shaders does not work with anaglyph and might this
be improved later?
Again, modern shaders do indeed work with PyMOL–I use them all the
time–your video card just has to be good enough and you need to be
using PyMOL v1.5 or later.
Cheers,
-- Jason
From: Jason Vertrees jason.vertr...@schrodinger.com
Date: Wednesday, 26 June 2013 21:53
To: Gary Hunter gary.hun...@um.edu.mt
Cc: Thomas Holder thomas.hol...@schrodinger.com,
pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Anaglyph colours sorted (kind of)
Hi Gary,
1) do not use a black background
Agreed. Something like gray works well in my experience. Don't forget in
techniques like anaglyph and chromadepth color takes on another meaning–it
encodes depth or separation. It's useful to keep this in mind.
2) do not use setting rendering modernize
If you have a modern video card that supports shaders well, Setting
Rendering Modernize will give you better performance and much prettier
graphics. If, however, you're on a laptop with an old Intel graphics card,
stick to immediate mode rendering ('set use_shaders, 0').
3) be careful with setting quality too high (especially on spheres)
Again, using Setting Rendering Modernize will actually give you pixel
perfect spheres drawn quickly. But, in immediate mode, you are correct.
To create the highest-quality movies or images, make sure you ray trace your
images. This can be done with the 'ray', and 'png' commands or as movie
creation time if 'ray_trace_frames' is set.
To reinitialize PyMOL just run the reinitialize command.
Cheers,
-- Jason
On 18/06/2013 09:59, Thomas Holder thomas.hol...@schrodinger.com wrote:
Hi Gary,
actually PyMOL should be optimized for red/cyan and not green/magenta.
There is no option to change the colors, sorry.
In PyMOL 1.5 anaglyph has been improved and there are is an
anaglyph_mode settings which defaults to 4 (optimized anaglyph).
Other reasonable values are 3 (half-color) and 1 (gray).
http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
If you really need to change the colors, you could take the open-source
code and tweak the anaglyph_mode matrix in layer1/Scene.c
Hope that helps.
Cheers,
Thomas
Gary Hunter wrote, On 06/17/13 09:53:
Is there a way to customise the colours used in anaglyph stereo mode?
Anaglyph mode has been optimised for green/magenta glasses but I have
lots of red/cyan ones so I'd like to change the colours used if I can.
Gary
Prof. Gary J. Hunter,
Department of Physiology and Biochemistry
University of Malta, Msida, MSD 2080, Malta.
phone: +356 2340 2917
phone: +356 21316655 (secretary), Fax: +356 21310577
http://www.um.edu.mt/ms/physbiochem
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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Re: [PyMOL] Anaglyph colours sorted (kind of)
Hi Gary,
1) do not use a black background
Agreed. Something like gray works well in my experience. Don't forget in
techniques like anaglyph and chromadepth color takes on another meaning–it
encodes depth or separation. It's useful to keep this in mind.
2) do not use setting rendering modernize
If you have a modern video card that supports shaders well, Setting
Rendering Modernize will give you better performance and much prettier
graphics. If, however, you're on a laptop with an old Intel graphics card,
stick to immediate mode rendering ('set use_shaders, 0').
3) be careful with setting quality too high (especially on spheres)
Again, using Setting Rendering Modernize will actually give you pixel
perfect spheres drawn quickly. But, in immediate mode, you are correct.
To create the highest-quality movies or images, make sure you ray trace
your images. This can be done with the 'ray', and 'png' commands or as
movie creation time if 'ray_trace_frames' is set.
To reinitialize PyMOL just run the reinitialize command.
Cheers,
-- Jason
On 18/06/2013 09:59, Thomas Holder thomas.hol...@schrodinger.com
wrote:
Hi Gary,
actually PyMOL should be optimized for red/cyan and not green/magenta.
There is no option to change the colors, sorry.
In PyMOL 1.5 anaglyph has been improved and there are is an
anaglyph_mode settings which defaults to 4 (optimized anaglyph).
Other reasonable values are 3 (half-color) and 1 (gray).
http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
If you really need to change the colors, you could take the open-source
code and tweak the anaglyph_mode matrix in layer1/Scene.c
Hope that helps.
Cheers,
Thomas
Gary Hunter wrote, On 06/17/13 09:53:
Is there a way to customise the colours used in anaglyph stereo mode?
Anaglyph mode has been optimised for green/magenta glasses but I have
lots of red/cyan ones so I'd like to change the colours used if I can.
Gary
Prof. Gary J. Hunter,
Department of Physiology and Biochemistry
University of Malta, Msida, MSD 2080, Malta.
phone: +356 2340 2917
phone: +356 21316655 (secretary), Fax: +356 21310577
http://www.um.edu.mt/ms/physbiochem
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
--
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Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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Re: [PyMOL] PyMOL 1.6 pre-release announcement
Hi David, If you save a session file in the latest version of PyMOL there is never the expectation that prior versions can read that file. Such forward compatibility (of the older versions) is not supported. We do support, however, backward compatibility which is when newer versions of PyMOL read older session files. Cheers, -- Jason On Wed, Jun 19, 2013 at 4:18 PM, David Hall li...@cowsandmilk.net wrote: I still have this problem: session saved in 1.6 with a black background; opens in 1.5 (and earlier) with a red background Many of my collaborators use old versions of pymol, frequently installed onto their machines when they were bought X years ago, and this essentially makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at least not without getting weird e-mails asking why I have a sudden affinity for the color red). -David On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder thomas.hol...@schrodinger.com wrote: This is fixed in SVN rev 4032. Cheers, Thomas Thomas Holder wrote, On 06/15/13 10:45: Hi Rob, this has not been fixed yet, I'm really sorry. We'll look into this ASAP. It only affects the open-source code, apparently we missed something when syncing with the incentive codebase. Cheers, Thomas On Jun 14, 2013, at 9:23 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hello Thomas and David, Was there any resolution of this? I've just compiled the latest version from SVN and I have the same problem opening files created under version 1.5.0. This is on Debian testing (32-bit). Cheers, Rob On Fri, 2013-04-26 19:15 EDT, David Hall li...@cowsandmilk.net wrote: Hi Thomas, I'm running into issues with color compatibility between 1.6 and earlier versions when opening pses (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: Setting-Error: type read mismatch (color) 6 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 664 (b) background color disparity: saved in 1.5 with black background; opens in 1.6 with a white background saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red background These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, others who would like to beta test can use devel:languages:python repo in openSUSE: https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython -David -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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 -- 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] PyMOL 1.6 pre-release announcement
Bob, Sure, feel free to send those to Thomas. Cheers, -- Jason On Thu, Jun 20, 2013 at 9:06 AM, Robert Hanson hans...@stolaf.edu wrote: (yes, I meant forward compatibility there) Jason, in our 100+ PyMOL session files that we can now read into Jmol we have a few files that don't seem to have backward compatibility to PyMOL 1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and measurements. Should I just send them to you and/or Thomas? Bob On Thu, Jun 20, 2013 at 7:36 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi David, If you save a session file in the latest version of PyMOL there is never the expectation that prior versions can read that file. Such forward compatibility (of the older versions) is not supported. We do support, however, backward compatibility which is when newer versions of PyMOL read older session files. Cheers, -- Jason On Wed, Jun 19, 2013 at 4:18 PM, David Hall li...@cowsandmilk.netwrote: I still have this problem: session saved in 1.6 with a black background; opens in 1.5 (and earlier) with a red background Many of my collaborators use old versions of pymol, frequently installed onto their machines when they were bought X years ago, and this essentially makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at least not without getting weird e-mails asking why I have a sudden affinity for the color red). -David On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder thomas.hol...@schrodinger.com wrote: This is fixed in SVN rev 4032. Cheers, Thomas Thomas Holder wrote, On 06/15/13 10:45: Hi Rob, this has not been fixed yet, I'm really sorry. We'll look into this ASAP. It only affects the open-source code, apparently we missed something when syncing with the incentive codebase. Cheers, Thomas On Jun 14, 2013, at 9:23 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hello Thomas and David, Was there any resolution of this? I've just compiled the latest version from SVN and I have the same problem opening files created under version 1.5.0. This is on Debian testing (32-bit). Cheers, Rob On Fri, 2013-04-26 19:15 EDT, David Hall li...@cowsandmilk.net wrote: Hi Thomas, I'm running into issues with color compatibility between 1.6 and earlier versions when opening pses (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: Setting-Error: type read mismatch (color) 6 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 664 (b) background color disparity: saved in 1.5 with black background; opens in 1.6 with a white background saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red background These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, others who would like to beta test can use devel:languages:python repo in openSUSE: https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython -David -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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 -- 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr
Re: [PyMOL] Leapmotion ?
Hi Aurélien, We demoed the LeapMotion controller with PyMOL at the last ACS meeting. Getting it hooked up to PyMOL wasn't too hard, thanks to Thomas. In our hands it wasn't ready for routine use: it was very erratic. The device didn't do well in a real world setting as it would recognize all sorts of things as Pointables--like my watch or reflections. We are waiting for the platform to mature a bit more before diving back in. Do let us know of your progress, as it's a really neat device with interesting potential. Cheers, Jason On Wednesday, June 19, 2013, Aurélien Grosdidier wrote: Hi all, We're planning to try PyMol with the leap motion device (https://www.leapmotion.com/). Has anyone already succeeded to do so ? Best, Aurélien. -- 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 javascript:; ) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] PyMOL measurements
Hi Bob, We added this a year or two ago: set dynamic_measures, 1 In newer versions of PyMOL this is enabled by default. Cheers, -- Jason On Fri, May 31, 2013 at 8:27 AM, Robert Hanson hans...@stolaf.edu wrote: Is there a way to tie measurement ends to specific atoms, so that when the structure is tweaked, those measurements update automatically? -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to get cealign outputs for mulitple structures
Hi Jacob, Use the result from cmd.cealign and an alignment object. Here's an example: # fetch two proteins fetch 1cll 1ggz, async=0 # use a python block python # cealign the two structures and create a corresponding alignment object result = cmd.cealign(1cll, 1ggz, object=aln) # print out the values from the result print result.keys() for key in result: print %s: %s % (key, result[key]) # end the python block python end # now access those atoms in the alignment select 1cll and aln # or count the atoms in 1ggz and aln print cmd.count_atoms(1ggz and aln) Cheers, -- Jason On Thu, May 30, 2013 at 2:07 PM, Jacob Pessin jacob.pes...@einstein.yu.eduwrote: Hi all, can anyone suggest a straightforward way of collecting the cealign output in bulk, (RMS, #atoms compared), using alignto doesn't even print this to screen (I tried adjusting quiet=, to no avail). thanks in advance jacob https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554# https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554# -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to face cartoon
Hi DJ, It sounds like you're using the transparency setting instead of cartoon_transparency. For example instead of movie_fade transparency, 1, 0., 40, 1. you likely want movie_fade cartoon_transparency, 1, 0., 40, 1. Cheers, -- Jason On Fri, May 10, 2013 at 3:50 AM, Dhananjay dhananjay.c.jo...@gmail.com wrote: Dear all, I am trying to animate set of proteins. Each protein has two conformations. I wanted to show first confirmation as cartoon, followed by fade out it and fade in the second confirmation. I could use movie_fade.py script successfully, however, it fades the surface to cartoon. I just want to fade out first confirmation and fade in and display the second one. Any suggestion please. Thanking you in advance. -- DJ -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ 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] trouble with fading for sticks in a movie
Hi Yarrow, set_bond stick_transparency, 0.5, myObj Cheers, -- Jason On Fri, Apr 26, 2013 at 11:03 AM, Yarrow Madrona amadr...@uci.edu wrote: Hi, I have previously been able to do a fake fade on surface transparency by doing the following: where testout is an object in pymol. mdo 449: set transparency, 1, testout mdo 550: show surface, testout mdo 551: set transparency, 0.7, testout mdo 552: set transparency, 0.6, testout mdo 553: set transparency, 0.5, testout mdo 554: set transparency, 0.4, testout mdo 555: set transparency, 0.3, testout mdo 556: set transparency, 0.3, testout mdo 557: set transparency, 0.1, testout mdo 558: set transparency, 0, testout The surface will slowly come to life between frames 449 and 558. However, if I try doing this with set stick_transparency, nothing happens. I have tried to do this using scenes, however the object simply disappears instead of fading. I would love some help on this. I am interested in python scripting as well as I know a little python but not sure how to implement it in pymol. Thanks! - Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Problems with H_add when theres alternate conformations present
Hi Esben, It's up to you to decide how you want to handle this. You have a few options. You can remove unwanted alternate conformations, for example: remove not alt ''+'A' then run your script. Or you can specify PyMOL only add hydrogens to a certain set of conformations: # only h_add to alt conformations labeled 'C' h_add 1zw9 and alt 'C' To only add hydrogens to default or 'A' conformers do the following: h_add 1zw9 and alt ''+'A' Cheers, -- Jason On Thu, Apr 18, 2013 at 3:59 AM, Esben Jannik Bjerrum esbenjan...@rocketmail.com wrote: Hi Pymol Users I have a problem with wrong atom assignment, and subsequently wrong addition of hydrogens, if theres alternate conformations present. I hope anyone else has experience with this or suggestions for troubleshooting. I have developed some scripts that downloads pdb-files from a list, add hydrogens to them, and otherwise prepares them for further usage. However, if theres alternate conformations present, the atoms on the backbone gets a wrong charge assignemt or something, breaking the subsequent addition of hydrogens. It seems to happen at PDB load time. Example steps to reproduce fetch 1zw9 zoom resi 12 h_add 1zw9 the hydrogen on the nitrogen in the backbone peptide bond doesn't make a planer configuration, and if I save the object, the oxygen is assigned a -1 charge. This makes troubles in my subsequent workflow. I've tried to delete the alternate conformations inside PyMOL before adding hydrogens, but that doesnt fix the problem. I can fix the problem by removing the alternate conformations from the PDB file before I load it into pymol, but I would rather fix it inside pymol in my scripts. Best Regards Esben Jannik Bjerrum -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ 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] CEalign parameter d0 and d1
Hi Quyen, It's been a few years since I wrote that but here is what I recall: D0 is a constant cutoff that represents the upper bound of dissimilarity for the difference of two distance matrices A_i and B_j, rooted at subsequences i to i+8 and j to j+8, respectively. Raising this value allows for sloppier fragments being considered. D1 is a constant cutoff that represents the upper bound of dissimilarity for the entire path being considered. In fact, it's equal to path_score / (window_size * path_length). So, D0 ensure that incoming fragments are still good. D1 ensures that as we extend the current alignment the total quality of the current alignment remains good. After this, all N top scoring paths are stored in the path cache and the best path is returned. Cheers, -- Jason On Wed, Apr 17, 2013 at 3:34 AM, QT rdirect...@gmail.com wrote: Dear all, I have a question regarding CEalign d0 and d1 parameter. What exactly are their functions? I don't know enough C++ to decipher the algorithm but they are used findPath() in ccealignmodule.cpp. It seems that that d0 controls a similarity matrix and d1 the path length. A d1 below a certain number does indeed make cealign return RMSD over smaller set of residues and there is a lower bound for d1 where cealign will fail to align. D0 behaves similarly. The default is 2 and 3 for d0 and d1. I'm going to guess that those numbers are also dimensionless. Will it be useful to tune the parameter d0 and d1? Best, Quyen -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ 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] CGO fixed in space
Hi Tim, We don't yet have advanced screen-stabilized objects. In the meantime consider, wizard message, Your Message Here Cheers, -- Jason On Mon, Apr 15, 2013 at 6:43 PM, Someone Else tno...@gmail.com wrote: Hi, is it possible to define a CGO object (e.g. a text) that wouldn't move when a user rotates the scene? For example, a graphics title in the top left corner Tim -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ 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] Howto fake mouse events in pymol
Hi Camilo, Currently we only offer this level of access via the C-library, so it's not accessible to end-users. The current workaround is to use the move and rotate commands. Cheers, -- Jason On Sun, Mar 31, 2013 at 10:31 AM, Camilo Andrés Jimenez Cruz camilo.jimen...@gmail.com wrote: Hi all. I am wondering if it is possible to fake mouse events in pymol. I would like to be able to simulate a click/drag in a specific position of the viewport. Thanks! -- Camilo Jiménez -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Invitation to visit at ACS New Orleans
Greetings, If you will be at the April ACS meeting in New Orleans, please feel free to stop by the Schrödinger booth (#400). I will be there much of the time answering questions, demoing new features, and generally discussing science and visualization. Specifically, we'll have a demo version of PyMOL v1.6, PyMOL on the iPad, and even a sneak peek of Leap Motion (https://www.leapmotion.com/) controller integration with PyMOL. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Invitation to visit at ACS New Orleans
Hi Sabuj, Do you have it working under linux? Yes, I have demonstrated the same functionality on Ubuntu (12.10). Ubuntu is the only Linux distro currently supported by Leap. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to hide the object control panel
Matthias, As David said, try setting internal_gui to 0. Or, try saving your session as a .psw instead of .pse. Cheers, Jason Sent from my Android. Please excuse the concision and any typos. On Mar 24, 2013 6:55 PM, Matthias Haffke matze_haf...@hotmail.com wrote: Dear all, this might be a simple question, but I would like to know how to hide the object control panel on the right side in the PyMol window. I would like to give a full screen presentation using scenes and it would be nice to have more space and remove the object control panel. Switching full_screen on does not do the job unfortunately - the object control panel remains visible. Many thanks already if anyone knows the solution, Matthias -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to ray trace clipped image without clipping spheres.
Hi Yarrow, This is a known problemhttp://sourceforge.net/p/pymol/feature-requests/53/. We'll try to fix this soon. Cheers, -- Jason On Mon, Mar 11, 2013 at 2:05 PM, Yarrow Madrona amadr...@uci.edu wrote: Hi, Does anyone know how to ray trace an image of an active site in sphere representation that is clipped, without getting a weird result that I assume comes from clipping the spheres? It looks like unfilled circles. Thank you -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-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] pymol install
Hi Yeping, Check out http://www.pymolwiki.org/index.php/Linux_Install#Compile_and_install. Cheers, -- Jason On Mon, Mar 4, 2013 at 8:17 PM, yp sun sunyep...@yahoo.com.cn wrote: Dear pymol users, I try to install pymol in Linux system as following (1) download pymol-v1.5.0.1.tar.bz2 and decompress it to /opt directory. (2) go into /opt/pymol/setup directiry and enter the command setup.sh Then I see the install success information: Creating ./pymol startup script with PYMOL_PATH=/opt/pymol/setup If you need to move PyMOL in the future, re-run ./setup.sh afterwards. You may now want to copy or link: /opt/pymol/setup/pymol to something like /usr/local/bin/pymol Enjoy! However, when I type pymol command, I get the error information: ./pymol: line 14: /opt/pymol/setup/ext/bin/python: No such file or directory ./pymol: line 14: exec: /opt/pymol/setup/ext/bin/python: cannot execute: No such file or directory Could you tell me why? Thanks! Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] How to visualize surface within a given radius
Greetings, Please also investigate the following settings: # needs a real atom selection surface_carve_selection # distance from the above selection to cull surfaces surface_carve_cutoff I looked at your data and there is a small problem. You have a few points where one atom is mapped to multiple surface points. Thus, when you show it as surface two pocket fragments show up. When you hide it they both hide. Also of interest is PyMOL's ability to render pockets and cavities on its own (Settings Surface Cavities Pockets). Cheers, -- Jason On Mon, Mar 4, 2013 at 2:15 PM, Sampson, Jared jared.samp...@nyumc.orgwrote: Hi Yarrow - If you add br. to the show surface command, you will get more continuous surfaces, as the selection will be made by residue instead of by atom. show surface, br. protein within 0.5 of pocket_selection If you don't want to show the surface from a particular residue (e.g. if it's masking something else you want to show), you can hide surface for a selection. hide surface, resi 225+347 Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 4, 2013, at 2:37 PM, Yarrow Madrona amadr...@uci.edu wrote: Thank you for your help Thomas, Using your settings I get a lot of partial surfaces Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow Hi Yarrow, should be as simple as: PyMOL hide surface PyMOL show surface, (organic around 8.0) PyMOL set transparency, 0.3 PyMOL set two_sided_lighting See also: http://pymolwiki.org/index.php/Selection_Algebra Hope that helps. Cheers, Thomas Yarrow Madrona wrote, On 03/03/13 18:34: Hello, Does anyone know how to visualize a surface within a given radius from a ligand binding site? In chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface surrounding the ligand without the rest of the protein. I guess you could create a new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 screenshot.png -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] Lighting script request
Hi Vitaly, In our later versions of PyMOL there's a setting called edit_light that controls which light may be moved by the mouse in 3-button Lights Mode. To enable 3-button Lights Mode, just click Mouse 3-Button Lights. Use shift+mouse to move the light around. To control which lights are being manipulated: # let there be 3 lights set light_count, 3 # move the second specular light set edit_light, 2 Now, in 3-button Lights mode, the mouse will move light 2. The default light is ambient which cannot be moved. If you have 3 lights on (ambient and two specular), then you can move the two specular two lights by setting edit_light to 1 or 2. Cheers, -- Jason On Sun, Feb 17, 2013 at 12:22 AM, V.V. vvos...@gmail.com wrote: Occasionally I need to play around with the number of lights and their vectors to get nice rendering. It's not something I do often, so every time I need to scour through the mailing list to recall Pymol definitions of light sources (the page on light badly needs updating). So... Can someone write a script that would grab the light data from the settings and present it as a separate object? A reverse action, where dragging the points of the light vector would update the lightX values would also be nice. Thank you, Vitaly -- The Go Parallel Website, sponsored by Intel - in partnership with Geeknet, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials, tech docs, whitepapers, evaluation guides, and opinion stories. Check out the most recent posts - join the conversation now. http://goparallel.sourceforge.net/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- The Go Parallel Website, sponsored by Intel - in partnership with Geeknet, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials, tech docs, whitepapers, evaluation guides, and opinion stories. Check out the most recent posts - join the conversation now. http://goparallel.sourceforge.net/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Zoom + Fading simultaneously in movie
Hi João, You'll need to use the mdo command to fade while zooming. The easiest way is to use the movie_fades script ( http://www.pymolwiki.org/index.php/Movie_fade) from the PyMOLWiki. Cheers, -- Jason On Sat, Feb 9, 2013 at 4:48 AM, João Rodrigues anar...@gmail.com wrote: Hi all, I'm trying to make a short movie here and I came across something I can't find on the internet how to do it.. I want to zoom in a region of the protein (done easily) and at the same time fade its surface (also easily done on its own, thanks Tsjerk). Is this possible or we cannot have two actions in the same frame? Sorry for the limited jargon for movie making! Best, João -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] Managing Viewport Location
Hi Wilson, The following works for me: # put the PyMOL window at 100,100 on startup ./pymol -X 100 -Y 100 I don't think we can programmatically move the OpenGL window once it's started up, however. On MacOS X 10.8 and the windowing system overrides these values; Linux and Windows should operate correctly. Cheers, -- Jason On Fri, Feb 8, 2013 at 4:04 PM, Wilson Omesiete womesi...@gmail.com wrote: Is it possible to control the screen location of the viewport during run time through the API? Currently I am using... import os, wx, __main__ app = wx.App() os.environ['PYMOL_PATH'] = C:\Python27\PyMOL __main__.pymol_argv = [ 'pymol', -qx] # Quiet and no GUI import pymol pymol.finish_launching() app.MainLoop() ...to load PyMol without the external GUI in quiet mode. I tried passing -qxX 30Y 50 in argv, but that change causes PyMol to load forever, also that would only give control over the initial position if it worked. -- Wilson Omesiete School of Biochemistry Georgia Institute of Technology -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] cross hair for non-bonded atoms
Hi Pascal, hide nonbonded Cheers, Jason Sent from my Android. Please excuse the concision and any typos. On Jan 30, 2013 1:10 PM, Pascal Auffinger p.auffin...@ibmc-cnrs.unistra.fr wrote: Hi, Just wondering how to remove the cross hair that is shown for each non-bonded atom (for example water molecules). Thanks, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr - -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ 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] Hight-quality visualisation
Hi James, In particular I wounder to know how I could decrease width of contour black line (appeared in set ray_trace_mode) ? Please modulate the ray_trace_gain setting to adjust the thickness of the outline. Please do not rely upon 3rd party software until you've tried this easier solution. For other neat rendering tricks, please see the PyMOLWiki's Gallery ( http://www.pymolwiki.org/index.php/Gallery). Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Active stereo on an iMac?
Hi Joachim, To my knowledge Apple does not support stereoscopic 3D. This has been a longstanding issue they still refuse to address. Cheers, -- Jason On Fri, Jan 25, 2013 at 11:34 AM, Joachim Reichelt joachim.reich...@helmholtz-hzi.de wrote: Dear Mac-User is it possible to use active stereo, e.g. NVIDIA shutter glasses + ASUS 3D Monitor on the latest iMac? The GT 640M/650M are on the list under http://www.nvidia.de/object/3d-vision-requirements-de.html -- Joachim Reichelt -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Piecewise rotations while viewing in surface
Hi Alex, We'll look into making this faster/smarter. To let you know, whenever you move an atom, it deforms the surface and causes a recalculation. The bigger your structure and higher quality the surface the longer this takes. Cheers, -- Jason On Tue, Jan 22, 2013 at 10:34 AM, Alex Truong atru...@bu.edu wrote: Hi All, This isn't really a problem per se, I'm just wondering. Is there any way to more efficiently code the rotation protocol when the items being viewed are in surface view? Maybe my computer isn't fast/strong enough or something, but it seems whenever I try tweaking the position of one subunits in relation to other subunits while everything is in surface view, two redraws occur, and it's difficult for me to adjust with precision because there's so much latency between positionings. Just a thought. again, it's not really much of an issue, because I can just retoggle a new view or something as a workaround, but it seems like manipulations while in surface view can get a little GPU/CPU intensive. Are the redraws necessary? Alex -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] names of the residues
Hi Ahmet, If your PDB is named 1foo and has one chain this should work: iterate first 1foo and poly, resn iterate last 1foo and poly, resn Otherwise you'll need to specify the selection more carefully, but first and last should still be appropriate. Cheers, -- Jason On Fri, Jan 25, 2013 at 4:16 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, How can I learn the names of the residues that make up the N- and C- terminals of a structure using Pymol? Thanks in advance -- Ahmet Yıldırım -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] new line in label
Hi Abhinav, It's currently not feasible. Please see the previous discussion on this: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08942.html. Cheers, -- Jason On Thu, Jan 24, 2013 at 11:04 AM, Abhinav Kumar abhin...@slac.stanford.eduwrote: Hi, I want to create a label that has a line break inside it. For example Asn\n102. Is there a way to do it? The command 'label selection Asn\n102' does not work. -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Write vector graphics of session
Greetings, There seems to be some significant interest in vector graphics output. To track this, I created a poll on the PyMOL website (http://pymol.org/vector_poll) where you can cast your vote on which format you prefer. Poll results will help advise development efforts. Cheers, -- Jason On Tue, Jan 15, 2013 at 6:32 AM, Martin Hediger ma@bluewin.ch wrote: I'm no expert but I guess my favorite would be EPS. Converting to PDF, if required, is easy on the Mac. Best regards Martin On 14.01.13 23:53, Jason Vertrees wrote: Martin, That would be a nice feature. Which format would you and the others prefer: SVG, PDF, or EPS? Cheers, -- Jason On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger ma@bluewin.ch wrote: Hi PyMOL users Can PyMOL write a vector based picture of a session? Does not require to be very fancy, but vector based would be cool. Something like in the old days with molscript. Best regards Martin -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122912 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ 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] Write vector graphics of session
Martin, That would be a nice feature. Which format would you and the others prefer: SVG, PDF, or EPS? Cheers, -- Jason On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger ma@bluewin.ch wrote: Hi PyMOL users Can PyMOL write a vector based picture of a session? Does not require to be very fancy, but vector based would be cool. Something like in the old days with molscript. Best regards Martin -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122912 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] stick/ribbon rendering not working
Hi Abhinav, Does this setting help: set cylinder_shader_ff_workaround, 1 If not, can you please send me a screenshot showing the problem? Cheers, -- Jason On Wed, Jan 9, 2013 at 5:40 PM, Abhinav Kumar abhin...@slac.stanford.edu wrote: Hi, I recently upgraded my desktop to Ubuntu 12.10. When I load a pdb in pymol, it comes up with line rendering as usual, but if I try to do a stick or ribbon rendering, it does not do it. In fact the stick operation hides the residue. These are the graphics specifics written by pymol. OpenGL graphics engine: GL_VENDOR: nouveau GL_RENDERER: Gallium 0.4 on NV84 GL_VERSION: 3.0 Mesa 9.0 Detected 4 CPU cores. Enabled multithreaded rendering. Any help please. -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] unittest for get_coordinate function
Hi Martin, I wonder, what is a most meaningful way of programmatically determining that a line of text in an arbitrary file contains atomic coordinates? The context of this question is that I plan to write a program that reads two files containing coordinates and has to perform operations on pairs of coordinates r1 and r2, where ri is the coordinate value from file i. [snip] You ask about reading and testing coordinate data from files in various formats. There are two things I can think of to consider. First, each file format will have a different definition and therefore properties for extracting data. Some, like the PDB will be column-based, so you'll need to focus on getting your columns exactly right. Others might be binary (MTZ) or dictionaries (CIF) in which higher-order parsing might be necessary. Thus, for each format, you'd need a specific test which will be defined by that format. Second, and this happens all the time, many application writers will produce files that are nearly properly formatted--read incorrectly formatted--and will break a strict parser. If you're working on a large set of files, I suggest you write a scrubber that you can apply across your files to ensure they're properly formatted before use. If you're lucky, your format will come with a nicely defined BNF grammar. Good luck. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Atom renaming within selection
James, alter my_sele, name=CA PyMOL might act quirky after doing that, though. Cheers, -- Jason On Thu, Jan 3, 2013 at 8:37 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! I want to rename all atoms within selection to the selected name. I've found that the renamecommand can do it but the syntax of that comand is not quite understood for me :( Could you provide me with some example ? e.g my mollecule consist of 120 carbon atoms named as the C1, C2... C120. I want to rename all atoms to CA ( the same index for all atoms). Thanks for help James -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Memory not released after load and delete of structure
Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote: Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Memory not released after load and delete of structure
Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote: Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote: Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] wierd bug in Ubuntu 12.10
Hi Stephan, I use Ubuntu 12 and haven't had any problems with PyMOL. I do have problems with my mouse in all apps, but that's not PyMOL's fault. Do you know anyone else with these problems? Have you asked around the Ubuntu community? Cheers, -- Jason On Sun, Dec 16, 2012 at 10:37 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear All, I have a wierd bug with pymol after a recent update to Ubuntu 12.10. If I use any auxiliary (not in pymol) software such as notepads, gedit, etc..Pymol then does some sort of switch if it is open at the same time for selections. It changes from residue, to atom, to whole molecule in the selection, depending on how much or how many times you go and type something in gedit. It then does not allow you to rotate the molecule, or change the menu selections anymore. I then have to re-start the computer, or re-install pymol to re-set the normal operations. This is extremely problematic, as pymol is a good program to quickly look at specific residues, etc...when doing massive text based tabulations of specific residues, and a necessary orientation and check visually is needed on the side to keep track of things. Needless to say the uses for anything else, such as making images, etc.. Has anyone experienced this, or more importantly, does anyone have a patch or bug fix. Sincerely, Stephan Watkins -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] what is an object colored ?
Hi Jon, ive been given a pse file.and i am trying to work out what color an object is.. i used the command get cartoon_color, pT_A and got back get: cartoon_color = default in object pT_A You're right, that's not very helpful. This will get you the answer, but it's not very straightforward: s = cmd.get_session() print cmd.get_color_tuple(s[names][1][5][0][2]) To make sure you have right object ensure that, s[names][1][5][0][1] equals your object name. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] make bond between two atoms
Hena, I created two objects as follows: pseudoatom A1, pos=[10.0, 10.0, 100.0] pseudoatom A2, pos=[10.0, 10.0, -200.0] I want to create a bond between these two atoms. Could you please help me? I need to display a 2 fold axis passing through these points. You can create a distance measure between them as shown here, http://www.pymolwiki.org/index.php/Pseudoatom. Or you can do this: pseudoatom foo1, pos=[0,0,0], name=CA pseudoatom foo2, pos=[1,1,1], name=CB create foo, foo1 or foo2 bond fooCA, fooCB which creates a single object from the two pseudoatoms and bonds the two pseudoatoms. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Help with alignments
Hi Jon, align prot1 and chain A, prot2 and chain X 'super' and 'cealign' should work similarly. Cheers, -- Jason On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes jonat...@strubi.ox.ac.uk wrote: I am wanting to align proteins based on superposition of particular chains. Is it possible to do the superposition based on the chains, but to move, in this case the entire complex ??? Thanks Jon Sent from my iPad -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Rendering memory errors
Hi Stephan Lloyd Watkins, I am no longer able to use the rendering plugin , which is a vlauble asset as I am at this moment in the midst of making some publication quality figures. Which rendering plugin are you referring to? What type of computer are you using? Additional, the standard ray trace option will only work if I use a white background, and zoom out further than would make a good image, ie a 300 amino protein about 1 inch square on an 8x8 inch window (visual field). How are you ray tracing? Using the 'ray' command? Clicking the 'ray' button? What happens if you do not use a white background? These bugs sound like they're related to the plugin, not PyMOL itself. Can you share your PyMOL session file with me? As it is both the rendering types, I assume it is some change to memory utilized by the shaders, as it crashes everytime. I have a similar problem now with gimp as well, however the memory cap is easy to see and maxes out around 3-4 G before crashing, however there is a 16 G memory, along with 4G on the GPU so I do not know where the errors come from. I do not get the errors on VMD, however prefer Pymol for the ease of use and also the images are nice. If you have Intel-based hardware you might try the following settings upon startup: set use_shaders, 0 set sphere_mode, 0 and then try your rendering plugin. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Project Upgrades
Greetings, This is just a quick note to let you know that the server hosting the PyMOLWiki has recently been upgraded. In general the site should be faster. If you see any problems, please let me know. If anyone is curious, the PyMOLWiki is still highly utilized. It's been viewed over 9.6 million times and often gets more than 2,000 unique visitors each day. Next, we've upgraded the open-source project page on SourceForge. Please be aware that some links will have moved. Likewise, if you see any problems, please let us know. The conversion will probably take a little time, so please be patient. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
Hi Rye, set connect_cutoff, 0.5 load 1.xyz produces different bonding than if you left the connect_cutoff value to its default, 0.35. Set it to 0.85 and then load the file and you'll see the Unknown atoms in the middle bonded as well. Cheers, -- Jason On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell ryeterr...@ryeterrell.net wrote: Hi Jason, Thanks for the tip. I still couldn't get it to work. I'll google around some more, but here's the file. Thanks for any help. Cheers, Rye On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Rye, How about connect_cutoff in Å? There's also connect_mode (http://www.pymolwiki.org/index.php/Connect_mode). If you send me a copy of your file I can look at it. Cheers, -- Jason On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell ryeterr...@ryeterrell.net wrote: I have a silicon bulk system. Pymol indicates that a handful of the atoms are bonded to each other. Many bonds are not indicated. Is there some value I can adjust that will make pymol indicate that more atoms are bonded? I usually do this by setting some cutoff radius, but googling around has yielded no results. I see that there is a way to bond atom pairs manually, but that would be incredibly tedious given the number of bonds there should be. Thanks for any help! Rye -- Keep yourself connected to Go Parallel: BUILD Helping you discover the best ways to construct your parallel projects. http://goparallel.sourceforge.net ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded
Hi Rye, How about connect_cutoff in Å? There's also connect_mode (http://www.pymolwiki.org/index.php/Connect_mode). If you send me a copy of your file I can look at it. Cheers, -- Jason On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell ryeterr...@ryeterrell.net wrote: I have a silicon bulk system. Pymol indicates that a handful of the atoms are bonded to each other. Many bonds are not indicated. Is there some value I can adjust that will make pymol indicate that more atoms are bonded? I usually do this by setting some cutoff radius, but googling around has yielded no results. I see that there is a way to bond atom pairs manually, but that would be incredibly tedious given the number of bonds there should be. Thanks for any help! Rye -- Keep yourself connected to Go Parallel: BUILD Helping you discover the best ways to construct your parallel projects. http://goparallel.sourceforge.net ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] iPad pymol questions
Hi Steve. I am a new subscriber to the pymol listserv. I did look around a bit on the listserv site, but did not find a way to search previous postings and responses, so did not find if there is a known answer to my question. Welcome to the PyMOL community. Minor question: is there a way to search the pymol message archive, and if so, how to do it? Yes, try here http://sourceforge.net/search/?group_id=4546type_of_search=mlists. You get there by mousing over Mailing Lists on the pymol-users archive page (http://sourceforge.net/mailarchive/forum.php?forum_name=pymol-users). Major question: I have been playing with the iPad version of pymol from Schrodinger. I know how to search pbd for structures,and how to view structures I have already found and saved to my pymol app folder on Dropbox. But I need to show some structures to an audience where I may not have wifi access for my iPad, and I would like to have the pymol iPad app locally save structure files so I can use them when I am off line. Is there a way to do this with the iPad? Currently you need to be online to access your data. We'll fix this for the next release. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Keep yourself connected to Go Parallel: INSIGHTS What's next for parallel hardware, programming and related areas? Interviews and blogs by thought leaders keep you ahead of the curve. http://goparallel.sourceforge.net ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
Mike, Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case, what pymol facilities are there for adding them? Apparently you have some editing h_add object_name Type, help h_add or check out h_add on the PyMOLWiki (http://www.pymolwiki.org/index.php/H_Add). Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, 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] ribbon trace, visualizing polymers (resent)
Hi Erik, Can you please send me a copy of one of the problematic sessions? Cheers, -- Jason On Tue, Nov 27, 2012 at 11:23 AM, Erik Nelson nelsoner...@gmail.com wrote: I use pymol to generate images of simple polymers by loading their coordinates as .pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates. I connect them using the ribbon_trace option, and color them by varying b-factors in the .pdb file. I had created many different movies and figures this way, and I saved the sessions as .pse files. Just recently, I went back to view some of these sessions and they just loaded as blank screens. I tried creating more images as before - using the ribbon_trace option to connect the atoms - but it no longer works. I'm pretty sure I didn't change any options in pymol, so I'm wondering if pymol somehow updated itself, or some update of my mac airbook affected the pymol program. Neither of these seems very likely. What went wrong? Is there a way I can fix this? A more general question. It seems like there must be a better way to visualise a polymer, say as a ball an stick image. Is there a more straight forward way of doing this in pymol? Thanks, Erik -- Erik Nelson Howard Hughes Medical Institute 6001 Forest Park Blvd., Room ND10.124 Dallas, Texas 75235-9050 p : 214 645 5981 f : 214 645 5948 -- 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, 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] ribbon trace, visualizing polymers (resent)
Hi Erik, This is a known bug introduced in OS X 10.8 and some video cards. To fix this just type, set cylinder_shader_ff_workaround, 1 and all should be well. PyMOL uses an official rendering optimization but some systems have difficulty with it, hence our workaround. This is automatically fixed in PyMOL v1.5.0.5 and later (and in the recent open-source code). Cheers, -- Jason On Tue, Nov 27, 2012 at 11:23 AM, Erik Nelson nelsoner...@gmail.com wrote: I use pymol to generate images of simple polymers by loading their coordinates as .pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates. I connect them using the ribbon_trace option, and color them by varying b-factors in the .pdb file. I had created many different movies and figures this way, and I saved the sessions as .pse files. Just recently, I went back to view some of these sessions and they just loaded as blank screens. I tried creating more images as before - using the ribbon_trace option to connect the atoms - but it no longer works. I'm pretty sure I didn't change any options in pymol, so I'm wondering if pymol somehow updated itself, or some update of my mac airbook affected the pymol program. Neither of these seems very likely. What went wrong? Is there a way I can fix this? A more general question. It seems like there must be a better way to visualise a polymer, say as a ball an stick image. Is there a more straight forward way of doing this in pymol? Thanks, Erik -- Erik Nelson Howard Hughes Medical Institute 6001 Forest Park Blvd., Room ND10.124 Dallas, Texas 75235-9050 p : 214 645 5981 f : 214 645 5948 -- 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Keep yourself connected to Go Parallel: DESIGN Expert tips on starting your parallel project right. http://goparallel.sourceforge.net ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
Hi Mike, I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. We have an API for accessing structures remotely. For example, load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb, myMolecule You could easily create a PyMOL plugin (http://www.pymolwiki.org/index.php/Plugins_Tutorial) that takes advantage of this site very simply using the load command and formatted URLs. I hope your meal was tasty. Cheers, -- Jason From: jason.vertr...@schrodinger.com Date: Fri, 2 Nov 2012 18:57:38 -0500 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mobile PyMOL Problem and Solution Greetings, On Oct 28th, the folks at the PDB made some changes to their PDB Web Services interface. This change broke Mobile PyMOL's ability to search for and download PDBs. I haven't bothered to look at this specific situation but this a problem with many sites and automated interaction. NCBI has a nice eutils interface that has remained stable for a while, I'd been trying to get more groups to offer a web interface designed for automated interactions. FWIW, http://www.ncbi.nlm.nih.gov/books/NBK25500/ Do you have automated access to this library for example, http://www.ncbi.nlm.nih.gov/Structure/index.shtml they also have their own viwer, for example, http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml but pymol seems a bit more extensive. I have updated Mobile PyMOL and will soon resubmit it to the AppStore for verification and release. This process takes typically takes no less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users please use the following technique to acquire structures: (1) Using Safari on the iPad browse to the www.pdb.org and find the structure you want. (2) Click Download Files from the upper right hand side of the structure's page and then select PDB File (Text). (3) Click Open in PyMOL. Happily, as a long-term solution, I've established contact with the PDB Web Services Group and we'll now be made aware of future changes. The PDB is an extremely valuable resource in the community and I'm glad we could work this out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, 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] Pymol in command mode - no output
Hi Per, You'll probably want to use something like this: # load the file load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb, myMolecule # ray trace and save the image; you need to do this since you're running # PyMOL headlessly png ~/foo.png, height=768, width=1024, ray=1 As far as missing output that's most likely because you're running remotely and the stdout/stderr are being piped elsewhere. This is common on clusters. Cheers, -- Jason On Mon, Nov 26, 2012 at 10:28 AM, Per Larsson per.lars...@sbc.su.se wrote: Hi Pymol-users, I'm running a pml-script file to render some images on a remote server, using pymol 1.4, but I do not get any output at all. And no error message, so it is hard to troubleshoot, unfortunately. To reduce the complexity of my script, I have reduced it to basically just loading a pdb-file and saving as a png-image (two lines in the pml-script), but even that does not work. Any suggestions? I envoke the whole thing using $pymol -c script.pml Thanks /Per -- 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, 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] cgo object tutorials
Hi Heng, Hi, I am just wondering if there are some useful pymol cgo tutorials available ? such as how to visualize a 3D triangle object(vertex and triangle files are known ) in Pymol? See https://www.google.com/?q=pymol%20cgo. There is a chapter subsection on CGOs and also a few scripts the demonstrate their usage. In addition, is the pymol volume visualize (http://pymol.org/volume) available for educational use ? Volume visualization is available in the Incentive version and open-source builds, but not the free Educational version. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, 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] (no subject)
Hi Mary, Just a hint for any future lists you might be on: most modern email lists, including pymol-users, have footers with links to subscription options. You simply click that to get to a subscription page where you can unsubscribe. In this case, I removed you from the list to save you the hassle. Cheers, -- Jason On Mon, Nov 26, 2012 at 5:30 PM, Mary Hall mh...@potomacschool.org wrote: How do I remove myself from the PyMOL users list? I'd like to stop receiving emails. Thank you. M. Hall -- 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, 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] sphere_scale
Hi Jon, I'm stumped too, because that's the correct syntax. Can you send me a copy of your session file? The only thing I can think of at present is that a selection might need: set sphere_scale, 5, (selection_name) Cheers, -- Jason On Mon, Nov 26, 2012 at 2:53 PM, Jonathan Grimes jonat...@strubi.ox.ac.uk wrote: I wanted to changed the size of sphere_scale for all atoms in an object, a selection of Calpha atoms. I thought I could use the command set sphere_scale, 5, object_name this doesnt seem to work and am unclear as to the reason. thanks jon does the command Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, 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
