Re: [PyMOL] sources for PyMOL 2
OK, I found the answer myself, googling in this email list. Sources will be released early next year, I understood. I'll wait patiently :) Cheers, Albert On 22/11/17 11:49, Albert Solernou wrote: Dear All, we have been writing a plugin for PyMOL during the last years, released as GPL. I would like to support PyMOL2, but need to know whether the code will be made accessible or not. Is PyMOL2 still free software? And if so, can we get access to the source code? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] sources for PyMOL 2
Dear All, we have been writing a plugin for PyMOL during the last years, released as GPL. I would like to support PyMOL2, but need to know whether the code will be made accessible or not. Is PyMOL2 still free software? And if so, can we get access to the source code? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] loading StringIO
That's lovely, David. Thanks, Albert On 10/26/2016 11:56 AM, David Hall wrote: > https://pymolwiki.org/index.php/Read_Pdbstr > > -David > > On Oct 26, 2016, at 3:55 AM, Albert Solernou <a.soler...@leeds.ac.uk > <mailto:a.soler...@leeds.ac.uk>> wrote: > >> Dear All, >> I was wondering if there was a way to load a PDB file stored in memory >> instead of disk, i. e., a memory file, defined through StringIO or >> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could >> handle an open file instead of a file? >> >> Thanks, >> Albert >> >> >> -- >> - >> Dr Albert Solernou >> EPSRC Research Fellow, >> Department of Physics and Astronomy, >> University of Leeds >> Tel: +44 (0)1133 431451 >> >> -- >> The Command Line: Reinvented for Modern Developers >> Did the resurgence of CLI tooling catch you by surprise? >> Reconnect with the command line and become more productive. >> Learn the new .NET and ASP.NET <http://ASP.NET> CLI. Get your free copy! >> http://sdm.link/telerik >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net >> <mailto:PyMOL-users@lists.sourceforge.net>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ PyMOL-users mailing list (PyMOL-users@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] loading StringIO
Hi Jordan, I still don't figure out how to do that with "load_object". What is the "type" for a file handler? Would be "object" the file handler itself? Albert On 10/26/2016 10:58 AM, Jordan Willis wrote: > Probably could use load_object instead. > > >def load_object(type,object,name,state=0,finish=1,discrete=0, > quiet=1,zoom=-1,_self=cmd): > ''' > DESCRIPTION > > "load_object" is a general developer function for loading Python objects > into PyMOL. >> On Oct 26, 2016, at 1:55 AM, Albert Solernou <a.soler...@leeds.ac.uk >> <mailto:a.soler...@leeds.ac.uk>> wrote: >> >> Dear All, >> I was wondering if there was a way to load a PDB file stored in memory >> instead of disk, i. e., a memory file, defined through StringIO or >> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could >> handle an open file instead of a file? >> >> Thanks, >> Albert >> >> >> -- >> - >> Dr Albert Solernou >> EPSRC Research Fellow, >> Department of Physics and Astronomy, >> University of Leeds >> Tel: +44 (0)1133 431451 >> >> -- >> The Command Line: Reinvented for Modern Developers >> Did the resurgence of CLI tooling catch you by surprise? >> Reconnect with the command line and become more productive. >> Learn the new .NET and ASP.NET <http://ASP.NET> CLI. Get your free copy! >> http://sdm.link/telerik >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ PyMOL-users mailing list (PyMOL-users@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] loading StringIO
Dear All, I was wondering if there was a way to load a PDB file stored in memory instead of disk, i. e., a memory file, defined through StringIO or tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could handle an open file instead of a file? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ PyMOL-users mailing list (PyMOL-users@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] selecting faces and vertices in CGOs
Hi Thomas, thanks for your answer. Even if it is challenging, I could still be interested in coding that. I have written a plugin for PyMOL that we plan to release as soon as it proves to be stable, together with another piece of software, and that functionality would help us very much. I would be very grateful if you could give me some hints on the code structure, and on how to tackle the inclusion of this new feature. Cheers, Albert On 04/08/2016 09:18 PM, Thomas Holder wrote: > Hi Albert, > > This is currently not possible and adding this would be a very major project. > > Cheers, > Thomas > > On 30 Mar 2016, at 10:40, Albert Solernou <a.soler...@leeds.ac.uk> wrote: > >> Dear All, >> I was wondering if there is a way to select faces, vertices and/or edges >> from a CGO either using the mouse or the command line. How difficult >> would be to add this, and how would you do that? >> >> It would be very useful for us if we could get that working. >> >> Thanks, >> Albert >> >> -- >> - >> Dr Albert Solernou >> EPSRC Research Fellow, >> Department of Physics and Astronomy, >> University of Leeds >> Tel: +44 (0)1133 431451 > -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ PyMOL-users mailing list (PyMOL-users@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] selecting faces and vertices in CGOs
Dear All, I was wondering if there is a way to select faces, vertices and/or edges from a CGO either using the mouse or the command line. How difficult would be to add this, and how would you do that? It would be very useful for us if we could get that working. Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/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] RMS over a MD trajectory.
Oh, I see... It looks like I'll need to end up writing a short script that does the loop along the trajectory together with a correct RMS calculation. Thanks for the tip, Carsten. Cheers, Albert On 05/08/2015 04:11 PM, Schubert, Carsten [JRDUS] wrote: Hi Al, based on my experience running align or super with cycles=0 has the tendency to produce inferior alignment results. So depending on how similar the conformation of your structures are you may end up with skewed statistics. What I've done in the past and for a paper I'm working on now is to run the alignment with default parameters to get the best superposition and then calculate the statistics by hand from the superposed structures. Not sure if cmd.rms() would do this for all residues w/o outlier rejection, so I ended up writing code for myself. The colorbyrmsd.py (http://pymolwiki.org/index.php/ColorByRMSD) script gives a nice illustration on how to approach this this. Carsten -Original Message- From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] Sent: Friday, May 08, 2015 10:04 AM To: Thomas Holder Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] RMS over a MD trajectory. Thanks Thomas, I was already printing k[i][3] (RMSD before refinement) instead of k[i][0] (RMSD after refinement) but your cycles=0 looks cleaner. Cheers, Albert On 05/06/2015 05:14 PM, Thomas Holder wrote: Hi Albert, Please pay attention to the difference between all-atom RMSD and RMSD after outlier rejection. http://pymolwiki.org/index.php/Align#RMSD If your trj and pdb1 have identical topology and matching atom identifiers, then you can also use cmd.rms(). http://pymolwiki.org/index.php/Rms Cheers, Thomas On 06 May 2015, at 11:56, Albert Solernou a.soler...@leeds.ac.uk wrote: Terribly useful Carsten! I could easily do a loop and get the RMS along the trajectory: k = [] for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i)) for i in range(100): print k[i][0] Cheers, Albert On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote: Hi Al, you would need to go through the Python API: python rms=cmd.align(mobCA,tarCA, quiet=0) print rms python end rms contains a tuple with various parameters related to the superposition. The first value in the tuple i.e. rms[0] should be the RMS value. HTH Carsten -Original Message- From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] Sent: Wednesday, May 06, 2015 8:32 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] RMS over a MD trajectory. Hi, I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I can see that align does things correctly when: align trj, pdb1, mobile_state=1 i. e., when I align the first snapshot of the trajectory with the PDB file. I also understand that PyMOL does compute the RMS along the trajectory if I simply: align trj, pdb1 as it is told in: http://www.pymolwiki.org/index.php/Align However, I am unable to get the list of RMS values printed out. How could I do that? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol
Re: [PyMOL] RMS over a MD trajectory.
Thanks Thomas, I was already printing k[i][3] (RMSD before refinement) instead of k[i][0] (RMSD after refinement) but your cycles=0 looks cleaner. Cheers, Albert On 05/06/2015 05:14 PM, Thomas Holder wrote: Hi Albert, Please pay attention to the difference between all-atom RMSD and RMSD after outlier rejection. http://pymolwiki.org/index.php/Align#RMSD If your trj and pdb1 have identical topology and matching atom identifiers, then you can also use cmd.rms(). http://pymolwiki.org/index.php/Rms Cheers, Thomas On 06 May 2015, at 11:56, Albert Solernou a.soler...@leeds.ac.uk wrote: Terribly useful Carsten! I could easily do a loop and get the RMS along the trajectory: k = [] for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i)) for i in range(100): print k[i][0] Cheers, Albert On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote: Hi Al, you would need to go through the Python API: python rms=cmd.align(mobCA,tarCA, quiet=0) print rms python end rms contains a tuple with various parameters related to the superposition. The first value in the tuple i.e. rms[0] should be the RMS value. HTH Carsten -Original Message- From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] Sent: Wednesday, May 06, 2015 8:32 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] RMS over a MD trajectory. Hi, I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I can see that align does things correctly when: align trj, pdb1, mobile_state=1 i. e., when I align the first snapshot of the trajectory with the PDB file. I also understand that PyMOL does compute the RMS along the trajectory if I simply: align trj, pdb1 as it is told in: http://www.pymolwiki.org/index.php/Align However, I am unable to get the list of RMS values printed out. How could I do that? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ PyMOL-users mailing list (PyMOL-users@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] RMS over a MD trajectory.
Hi, I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I can see that align does things correctly when: align trj, pdb1, mobile_state=1 i. e., when I align the first snapshot of the trajectory with the PDB file. I also understand that PyMOL does compute the RMS along the trajectory if I simply: align trj, pdb1 as it is told in: http://www.pymolwiki.org/index.php/Align However, I am unable to get the list of RMS values printed out. How could I do that? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ PyMOL-users mailing list (PyMOL-users@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] RMS over a MD trajectory.
Terribly useful Carsten! I could easily do a loop and get the RMS along the trajectory: k = [] for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i)) for i in range(100): print k[i][0] Cheers, Albert On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote: Hi Al, you would need to go through the Python API: python rms=cmd.align(mobCA,tarCA, quiet=0) print rms python end rms contains a tuple with various parameters related to the superposition. The first value in the tuple i.e. rms[0] should be the RMS value. HTH Carsten -Original Message- From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] Sent: Wednesday, May 06, 2015 8:32 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] RMS over a MD trajectory. Hi, I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I can see that align does things correctly when: align trj, pdb1, mobile_state=1 i. e., when I align the first snapshot of the trajectory with the PDB file. I also understand that PyMOL does compute the RMS along the trajectory if I simply: align trj, pdb1 as it is told in: http://www.pymolwiki.org/index.php/Align However, I am unable to get the list of RMS values printed out. How could I do that? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ PyMOL-users mailing list (PyMOL-users@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] unable to export obj
Hi, I am trying to get a .obj file, but fail when setting up surface_type to 2. More explicitly: load 1ppe.pdb, 1ppe set surface_type, 2 hide everything show surface shows a nice triangulated surface. However, save myscene.obj saves an empty file. I've tried pymol versions 1.7.4 and 1.6.0. Saving into an obj file works well when surface_type is set to 0, or 1. Any help? Best, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ PyMOL-users mailing list (PyMOL-users@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] rms_cur, rms, fit - No atoms selected
I'm new at pymol, and I'm trying to use the commands rms and rms_cur. I have two pdb files, with two proteins in each. First, I load the files load 1acb_321000.pdb, c321 load 1acb_dock.pdb, dock then I select the backbone of the B chain of each complex, select lc, /c321//b//ca+c+n+o select lr, /dock//b//ca+c+n+o Everything works until here. Each selection is showed on the screen, and they are 207 atoms each. Now I want to get the rms value without superimposing: rms_cur lc, lr but it does not work: ExecutiveRMS-Error: No atoms selected. It also does not work with rms or fit commands, although it works with align: align lc, lr Match: read scoring matrix. Match: assigning 69 x 69 pairwise scores. MatchAlign: aligning residues (69 vs 69)... ExecutiveAlign: 207 atoms aligned. ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=0.01). ExecutiveRMS: 2 atoms rejected during cycle 2 (RMS=0.01). Executive: RMS =0.006 (200 to 200 atoms) I've seen that someone has reported a bug at debian's, under the version 0.99rc6: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=486254 I've tried the 1.0r2-1 version (commming with ubuntu, apt-get), and compliling the source code from the svn of the current version, 1.2-x. Same results. Hope someone can help me, albert
