[PyMOL] PyMOLWiki Upgraded (again)
Greetings, I just discovered that the PyMOLWiki was failing due to memory limitations. I doubled the RAM on the instance and restarted it. We should be good for a while. Cheers, -- Jason -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/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] 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 While operating well, the site, schemas, and plugins were outdated.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 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 > 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&iu=/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 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 > 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&iu=/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: Quick Update
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&iu=/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
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%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0A&s=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%3B&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0A&s=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] 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 > 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 refuse<http://www.linkedin.com/in/jasonvertrees/>—to follow one of my dreams—helping lead technology and science at a new startup<http://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 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.gr > > teva...@gmail.com > > > website: > thomasevangelidishomepage<https://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=122218951&iu=/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 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=124407151&iu=/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=124407151&iu=/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=121051231&iu=/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 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=121051231&iu=/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=121051231&iu=/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=123612991&iu=/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=123612991&iu=/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=123612991&iu=/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=123612991&iu=/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 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=119420431&iu=/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=119420431&iu=/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 wrote: > 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=119420431&iu=/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 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=119420431&iu=/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=119420431&iu=/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 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=119420431&iu=/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=119420431&iu=/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 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=119420431&iu=/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=119420431&iu=/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 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 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=119420431&iu=/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=119420431&iu=/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 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=119420431&iu=/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=119420431&iu=/4140/ostg.clktrk___
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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=119420431&iu=/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 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=119420431&iu=/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=119420431&iu=/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
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]
> 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
Re: [PyMOL] Rendering in pymol
James, PyMOL can use multiple CPU cores to create ray-traced images. PyMOL does not ray trace on the GPU. If you enable use_shaders then you're getting graphics that are as good as ray tracing but without shadows or antialiasing. So, if that's okay for you, then calculate your viewport size, disable ray_trace_mode, and re-render your movie. Cheers, -- Jason On Fri, Nov 29, 2013 at 1:58 AM, James Starlight wrote: > Der Pymol users! > > I wounder to know if it possible to increase rendering rate mainly at the > expense of the GPU usage. At my desktop with core i7 and 6 cpu (12 cpus in > the hyper-threading mode) I've spend ~ 2 hours to render image consisted of > ensemble of conformations (~ 30 aligned pdbs) using only CPUs. > > set ray_trance mode, 1 > ray 3000 > png ./1.png > > > Does it possible to add some loading to the gpu as well? > > > James > > -- > 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=84349351&iu=/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 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=84349351&iu=/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] 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 wrote: > > 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 > 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=63431311&iu=/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 wrote: > 2013/11/24 Jason Vertrees : > > 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 > > 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=63431311&iu=/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=63431311&iu=/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 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=63431311&iu=/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=63431311&iu=/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 wrote: > 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=63431311&iu=/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=63431311&iu=/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 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=60136231&iu=/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=63431311&iu=/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 wrote: > 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=63431311&iu=/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=63431311&iu=/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 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=63431311&iu=/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=63431311&iu=/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 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=63431311&iu=/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=63431311&iu=/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 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=60136231&iu=/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=60136231&iu=/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 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=60136231&iu=/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=60136231&iu=/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 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 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=65839951&iu=/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=60136231&iu=/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=60136231&iu=/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=60136231&iu=/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 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=65839951&iu=/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=60136231&iu=/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=60136231&iu=/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 wrote: > 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=65839951&iu=/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=65839951&iu=/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 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=65839951&iu=/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=65839951&iu=/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 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 > wrote: >> >> Ok, I will try editing those files. >> >> Cheers, >> >> Osvaldo. >> >> >> >> On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees >> 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 >>> 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=60134071&iu=/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=60134071&iu=/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 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=60134071&iu=/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=60134071&iu=/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 (b<0.5 or b>0.5) 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=60134071&iu=/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=60134071&iu=/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] Announcing the 2013–2014 PyMOL Open Source Fellows
Greetings PyMOL users worldwide, Please join me in congratulating Tsjerk Wassenaar and Jared Sampson on their recent appointments as Warren L. DeLano Memorial PyMOL Open Source Fellows for 2013–2014. Dr. Tsjerk Wassenaar is a long-time PyMOL community member who will be working on extending PyMOL's abilities in the arena of visualization and analysis of ensembles. Jared Sampson will be working on extending PyMOL's capabilities in writing various 3D formats including COLLADA. This will help PyMOL interoperate better with 3D printing and other rendering programs. The Warren L. DeLano Memorial PyMOL Open-Source Fellowship is awarded by Schrӧdinger to supplement the income of an outstanding member of the PyMOL open-source community so that s/he can continue to develop free resources to help scientific progress and the community as a whole. You can read more about the PyMOL Open Source Fellowship Program and the fellows here http://pymol.org/fellowship. I look forward to seeing their code in action and its positive effects on the community. Cheers, -- Jason -- 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=60134071&iu=/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 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=60133471&iu=/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=60133471&iu=/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 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:
> PyMOL>set bg_gradient, 1
> PyMOL>get 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"
> An: "Nils NN"
> Cc: "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 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
>
>
>
>
>
> --
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> _______
> 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
--
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Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
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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 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
>
>
>
>
>
>
> --
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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 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=5127&iu=/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=5127&iu=/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] 3D Vision Performance
Hi Dan, The PDB 3ZLJ only has 13,233 atoms in the PDB. Recent versions of PyMOL _should_ be able to handle that in 3D with transparent surfaces and sticks just fine. I don't have an FX 4800, but have tested on similar hardware with larger systems successfully. Can anyone out there with a Quadro FX 4800 or similar comment on 3D performance with 3ZLJ? For what it's worth, in anaglyph 3D mode (which does double-rendering) for 3ZLJ, shown as described above, on a MacBook Pro with an NVidia GeForce 650M, I'm getting about 48 FPS. Cheers, -- Jason On Mon, Aug 26, 2013 at 10:59 PM, Dan Piraner wrote: > Hello all, > > If anyone is using PyMOL with NVidia's 3D Vision, I am wondering if > you could help me estimate performance with a prospective build. On > the PyMOL web site, the graphics card recommendations for 3D Vision > are as follows: > > 120Hz) NVidia 3D NVision with: >(entry) NVidia Quadro 580; entry level cards begin at approximately $99 >(better) NVidia Quadro FX 3800/4800 >(best) NVidia Quadro Q5000/Q6000 > > As someone used to quantitative benchmarks, I'm not exactly sure what > "entry", "better", and "best" actually mean. I'm thinking of pairing a > Quadro FX 4800 with an i7 4770k. I've never used a 3D Vision setup > before and am wondering what kind of performance to expect. Would it > be able to render a reasonably complex structure (picking at random, > 3ZLJ) with a transparent surface and stick representation without > lagging? > > Any quantitative information or suggestions would be greatly appreciated. > > Best, > > Dan > > > -- > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/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 -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/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] Fwd: Script writing
Hi James,
It could look something like this:
# for_rutley.py
# fetch a protein
cmd.fetch("1rx1", async=0)
# make a blank list
l=[]
# iterate over all lysine's alpha carbons
cmd.iterate_state(1, "n. CA and resn lys", "l.append((x,y,z))")
# set a counter to 0 for controlling unique names
p=0
# iterate over all coordinates and create a
# pseudoatom at each lysine's alpha carbon
for ca in l:
p+=1
cmd.pseudoatom("pseudo%s" % (p), pos=ca)
# measure the pairwise distances across all pseudoatoms just created
cmd.distance("/pseudo*", "/pseudo*")
I bet someone like Thomas or Tsjerk could code this in half the number of
lines, but this should be a starting point.
Cheers,
-- Jason
On Thu, Aug 22, 2013 at 9:55 AM, James Rutley wrote:
>
>
> -- Forwarded message --
> From: James Rutley
> Date: 22 August 2013 14:50
> Subject: Script writing
> To: pymol-users@lists.sourceforge.net
>
>
> Hi,
>
> I am new to Pymol and programming. What's the best way to approach
> creating a script that does the following:
>
> [image: Inline images 3]
>
> Thanks,
>
> James,
> UCL
>
>
>
> --
> Introducing Performance Central, a new site from SourceForge and
> AppDynamics. Performance Central is your source for news, insights,
> analysis and resources for efficient Application Performance Management.
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>
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Director of Core Modeling Products
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
<>--
Introducing Performance Central, a new site from SourceForge and
AppDynamics. Performance Central is your source for news, insights,
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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 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=48808831&iu=/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=48808831&iu=/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 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 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=48808831&iu=/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=48808831&iu=/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=48808831&iu=/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, 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 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=48808831&iu=/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=48808831&iu=/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 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: > --- > PyMOL>cluster_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 "", 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=48808831&iu=/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=48808831&iu=/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] 2013 PyMOL Open Source Fellowship–Request for Applications
Greetings PyMOLers, We have pushed back the deadline for the 2013 PyMOL Open Source Fellowship program to July 8th for those wishing to participate. If you like PyMOL, science, programming, and open-source here's your chance to give back. Students and postdocs are especially welcome to apply. For more information on the stipend, application rules, terms, etc., please see the main fellowship page on our website: http://pymol.org/fellowship. Cheers, -- Jason On Thu, Apr 25, 2013 at 9:31 AM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Greetings, > > I am delighted to announce that the 2013 PyMOL Open Source Fellowship > program is now accepting applications. Due to the success of the > program, we have two open spots this year. > > Application instructions and deadlines for the 2013 PyMOL Open Source > Fellowship have been posted here http://pymol.org/fellowship. > Interested applicants, please review the instructions before applying. > > The application deadline is July 1, 2013. > > Good luck! > > Cheers, > > -- Jason > > -- > 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 -- 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] cut protein in half
Hi Yeping, The technique will differ depending on the structure you have. Can you send me a copy and I can try to put something together for you? If it's a homodimer, usually we can just disable one unit and show the open channel. Also, see http://hollow.sourceforge.net/channel.html and http://www.pymolwiki.org/index.php/Biochemistry_student_intro#Movie_of_Epidermal_Growth_Factor . Cheers, -- Jason On Fri, Jun 28, 2013 at 2:14 AM, wrote: > > > > > Dear pymol users, > > I want to make a cross-section on a ion tunnel protein to cut it in half > and observe the intenal characters of the tunnel. According to materials on > web, I runed the following commands: > > hide all > show surfaceset ray_trace_mode, 0set two_sided_lighting, offset > ray_interior_color, grey50 > > > > But I didn't see any obvious change on the structure except that the protein > became dim. Could you help me with that? > > Tnanks in advance! > > > > Yeping Sun > > > > -- > 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 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
> Date: Wednesday, 26 June 2013 21:53
> To: Gary Hunter
> Cc: Thomas Holder ,
> "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" 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
>> >
>>
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"
> 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
> >
> >--
> >
> >This SF.net email is sponsored by Windows:
> >
> >Build for Windows Store.
> >
> >http://p.sf.net/sfu/windows-dev2dev
> >___
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> >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.
>
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>
--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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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 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 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 >>>> >> 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=pymol&project=devel%3Alanguages%3Apython >>>> >>> >>>> >>> -David >>>> >>>> -- >>>> Thomas Holder >>>> PyMOL Developer >>>> Schrödinger Contractor >>>> >>>> >>>> -- >>
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 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 >> >> 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=pymol&project=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] 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 > ) > 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 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
wrote:
> 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=Item&a=Open&t=IPM.Note&id=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIn&s=Draft&pspid=_1369930182703_402002554#>
> <https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIn&s=Draft&pspid=_1369930182703_402002554#>
>
>
> --
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Director of Core Modeling Products
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Re: [PyMOL] how to show ligand surface
John, fetch 1rx1, async=0 set surface_mode, 3 as surface, org Cheers, -- Jason On Mon, May 20, 2013 at 3:21 PM, John Quinn wrote: > Hi Troels, > > I've tried that in the past (and just tried again to make sure) but it > doesn't work for me. > > By the way, I'm running the latest open source version of PyMol installed > via fink on a Mac > > Yours &c. > > John Quinn > 133 Jay St. > Albany, NY 12210 > (518) 312-7033 > jqu...@uchicago.edu > > > > On May 20, 2013, at 4:03 PM, Troels Emtekær Linnet > wrote: > > Troels > > > > > -- > AlienVault Unified Security Management (USM) platform delivers complete > security visibility with the essential security capabilities. Easily and > efficiently configure, manage, and operate all of your security controls > from a single console and one unified framework. Download a free trial. > http://p.sf.net/sfu/alienvault_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 Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_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] how to show ligand surface
Hi, Extracting/copying the ligand is one way ( http://www.pymolwiki.org/index.php/Surface#Creating_a_Closed_Surface). You can also set surface mode (http://pymolwiki.org/index.php/Surface_mode) or flag a selection (http://www.pymolwiki.org/index.php/Flag). Cheers, -- Jason On Mon, May 20, 2013 at 3:03 PM, Troels Emtekær Linnet wrote: > Try to extract the ligand from the protein, so you get two separate > objects. > > Best > > Troels Emtekær Linnet > > > 2013/5/20 John Quinn > >> I have a question I've never been able to figure out. If I have a pdb >> file with a ligand bound in a protein I can show the protein as a mesh or >> surface but I can't ever show the surface of the ligand. Any advice? What >> am I missing? >> >> Thank you very much. >> >> Yours &c. >> >> John >> >> >> >> >> >> -- >> AlienVault Unified Security Management (USM) platform delivers complete >> security visibility with the essential security capabilities. Easily and >> efficiently configure, manage, and operate all of your security controls >> from a single console and one unified framework. Download a free trial. >> http://p.sf.net/sfu/alienvault_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 >> > > > > -- > AlienVault Unified Security Management (USM) platform delivers complete > security visibility with the essential security capabilities. Easily and > efficiently configure, manage, and operate all of your security controls > from a single console and one unified framework. Download a free trial. > http://p.sf.net/sfu/alienvault_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 Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_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] internal surface
Hi Yarrow, See demo #2 on the PyMOLWiki gallery page ( http://pymolwiki.org/index.php/Gallery). Cheers, -- Jason On Fri, May 10, 2013 at 5:42 PM, Yarrow Madrona wrote: > Hello pymol Gurus, > > I previously made a figure where the protien is cut in half and you can > see the ligand binding cavity. However, I have forgot how to reproduce it. > > My problem is that I want to show a slab of the internal surface not just > the interior part of the external surface. Can anyone help me with this? > > -Yarrow > > > -- > Yarrow Madrona > > Graduate Student > Molecular Biology and Biochemistry Dept. > University of California, Irvine > Natural Sciences I, Rm 2403 > Irvine, CA 92697 > > > > > > -- > 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 -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_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] Discrepancy between select within and distance?
Hi,
Folmer is correct on both accounts.
First, "select" was selecting across various states into one multistate
selection. Then, the distance command was operating on the first state,
which is its default behavior. So, replace
select asdf, 1MM2CA w. 5 of 2kgi///22/CA
with
select asdf, 1MM2CA w. 5 of 2kgi///22/CA, state=1
or whichever state you want and try again. (Or use Folmer's suggestion of
splitting out the states.)
Second, please don't hind behind a pseudonym. We don't bite.
Cheers,
-- Jason
On Sun, May 19, 2013 at 4:55 PM, asdf asdf wrote:
> Hello,
>
> I'm measuring the distance between certain residues in an alignment and
> I've noticed a discrepancy in the selections returned by the "select within
> command" and the actual distances measured to the atoms returned by the
> selection. I was wondering if maybe somebody knew where I was going wrong.
>
> When I run the following commands
>
> > fetch 1MM2
> > fetch 2kgi
> > align 2kgi, 1MM2
> > select asdf, 1MM2CA w. 5 of 2kgi///22/CA
> > iterate asdf, print(resi + " " + resn + " " + name + " " +
> str(cmd.distance("tmp", "2kgi///22/CA", "1MM2///" + resi + "/CA")))
>
> I get this output:
>
> 24 CYS CA 5.15101623535
> 25 ASP CA 3.34501266479
> 26 THR CA 6.03605747223
> 47 GLU CA 3.80576062202
> 48 TRP CA 3.85521435738
> 49 LEU CA 4.28281402588
>
> I'm just a little confused about why atoms that are further than 5
> angstroms away from the atom I specified in the select command are
> returned. Is there some difference in the way "select within" and
> "cmd.distance", or have a confused some of the commands?
>
> Any suggestions are appreciated
>
>
> --
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--
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
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security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
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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 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 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
[PyMOL] 2013 PyMOL Open Source Fellowship–Request for Applications
Greetings, I am delighted to announce that the 2013 PyMOL Open Source Fellowship program is now accepting applications. Due to the success of the program, we have two open spots this year. Application instructions and deadlines for the 2013 PyMOL Open Source Fellowship have been posted here http://pymol.org/fellowship. Interested applicants, please review the instructions before applying. The application deadline is July 1, 2013. Good luck! Cheers, -- Jason -- 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 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 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 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-Intel® 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-Intel® 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-Intel® 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" 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 problem<http://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 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] 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 wrote: > 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 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 > > > -- > > 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] 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 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] 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. 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 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 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] 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 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] 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 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] 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] 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 wrote: > 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 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 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 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] 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] Problem Opening Session File
Hi Pete, Versions of PyMOL before v1.5 will not be able to properly read maps in session files written by PyMOL v1.5 and later. We updated the map code to enable visualization of data beyond the unit cell, and added some new functions that allow you to copy symmetry and space group information from one object to another, because many times these data are missing or incomplete. Cheers, -- Jason On Tue, Jan 8, 2013 at 2:39 PM, Pete Meyer wrote: > The handling of density maps changed with (I believe) version 1.5 - > earlier versions would just load the map as given, later ones appear to > try to do symmetry expansion (even if the map isn't covering the ASU). > I've seen this result in a similar error message when loading session > files (with electron density, created in 1.4) with 1.5. My solution has > been to stick with 1.4. > > However, I don't generally use multi-state session files, so I don't > know if the electron density problem is related to the multi-state > problem or not. > > Pete > > Mike Feldkamp wrote: >> I created a session file with Pymol Version 1.5.0.4 that I am unable to open >> up on my laptop which is running 1.2r5pre. I am able to see the first state >> but all of the other remaining states are lost. I haven't had opening >> session files with saved states in the past so I do not suspect it is a >> issue of compatibility between versions. The one difference that I think is >> causing the problem is that the session contains an electron density map >> that does not appear to save along with the session. Below is the message >> that I receive from when I go to the state containing the density map. Has >> anyone else had this issue and been able to resolve it? If so how? >> This Executable Build integrates and extends Open-Source PyMOL >> 1.2r3pre.Warning: This session was created with a newer version of PyMOL >> (15.04).Warning: Some content may not load >> completely.ExectiveSetSession-Error: after names.ExectiveSetSession-Warning: >> restore may be incomplete.ObjectMeshUpdate-Error: map 'Density' has been >> deleted. >> Thanks,Michael >> >> >> >> >> >> -- >> 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 > > > -- > 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 -- 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] 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 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] 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 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
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 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 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
Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger 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 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
