Re: [PyMOL] DNA ligand presentation in PyMOL
Hi Amna, DNA molecule has internal HBONDS too.. how can i see the hbonds made between just ligand and DNA, ??? If there is nothing else than DNA and ligand, this should probably work (otherwise, be more precise with the selections...): PyMOL distance hbonds, (polymer), (organic), mode=2 how can i show just interacting residues of DNA with ligand i am unable to create this presentation.. PyMOL show sticks, (polymer) within 5 of (organic) Again, if polymer and organic are ambiguous, replace them with more explicit selections like (chain A and resi 34). http://pymolwiki.org/index.php/Single-word_Selectors http://pymolwiki.org/index.php/Selection_Algebra http://pymolwiki.org/index.php/Property_Selectors Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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] stick/ribbon rendering not working
Hi Abhinav, Does this setting help: set cylinder_shader_ff_workaround, 1 If not, can you please send me a screenshot showing the problem? Cheers, -- Jason On Wed, Jan 9, 2013 at 5:40 PM, Abhinav Kumar abhin...@slac.stanford.edu wrote: Hi, I recently upgraded my desktop to Ubuntu 12.10. When I load a pdb in pymol, it comes up with line rendering as usual, but if I try to do a stick or ribbon rendering, it does not do it. In fact the stick operation hides the residue. These are the graphics specifics written by pymol. OpenGL graphics engine: GL_VENDOR: nouveau GL_RENDERER: Gallium 0.4 on NV84 GL_VERSION: 3.0 Mesa 9.0 Detected 4 CPU cores. Enabled multithreaded rendering. Any help please. -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] get_dihedral for multiple files(states of a movie)
Hello all, I have generated a movie of 300 snapshots (MD simulation trajectory). How can i calculate dihedral angles for same four atoms across the trajectory (or a movie)?? I mean get_dihedral 58/n,58/c,58/ca,58/cb values 300 times for each snapshot. Regards Tasneem -- 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] get_dihedral for multiple files(states of a movie)
Hi Tasneem, python for state in range(1, cmd.count_states() + 1): angle = cmd.get_dihedral(58/N, 58/C, 58/CA, 58/CB, state) print state, angle python end Cheers, Thomas Tasneem Ali wrote, On 01/10/13 17:08: Hello all, I have generated a movie of 300 snapshots (MD simulation trajectory). How can i calculate dihedral angles for same four atoms across the trajectory (or a movie)?? I mean get_dihedral 58/n,58/c,58/ca,58/cb values 300 times for each snapshot. Regards Tasneem -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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] apbs2 plugin failure
Hi Andreas. The line: /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py shows that you are using the apbs tools from Michael G. Lerner. http://pymolwiki.org/index.php/APBS You might want to try out a little modified version of that. http://pymolwiki.org/index.php/Apbsplugin You might also want to try this. That is the repository with all scripts from Pymolwiki, to work out of the box. http://pymolwiki.org/index.php/Git_intro Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/1/3 Andreas Förster docandr...@gmail.com Dear all, on our RHEL computers (6.2, 64-bit) with PyMOL compiled from CVS, the APBS2 plugin isn't functioning anymore. The plugin window opens just fine and the executables are found. When I select Use PDB2PQR in the Main tab, clicking on Set grid produces the following error: Error: 1 type 'exceptions.UnboundLocalError' Exception in Tk callback Function: function lambda at 0x7fc2b0705410 (type: type 'function') Args: () Traceback (innermost last): File /usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line 1075, in execute self.runPsize() File /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line 1096, in runPsize good = self.generatePqrFile() File /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line 1007, in generatePqrFile good = self._generatePdb2pqrPqrFile() File /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line 1615, in _generatePdb2pqrPqrFile if retval != 0: type 'exceptions.UnboundLocalError': local variable 'retval' referenced before assignment When I chose User PyMOL generated PQR and PyMOL generated Hydrogens and termini or User PyMOL generated PQR and existing hydrogens and termini, I can set the grid, run APBS and visualize the result just fine. I'm happy with that, but maybe someone has an idea of why the first approach fails. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- 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 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] unittest for get_coordinate function
Hi Martin, I wonder, what is a most meaningful way of programmatically determining that a line of text in an arbitrary file contains atomic coordinates? The context of this question is that I plan to write a program that reads two files containing coordinates and has to perform operations on pairs of coordinates r1 and r2, where ri is the coordinate value from file i. [snip] You ask about reading and testing coordinate data from files in various formats. There are two things I can think of to consider. First, each file format will have a different definition and therefore properties for extracting data. Some, like the PDB will be column-based, so you'll need to focus on getting your columns exactly right. Others might be binary (MTZ) or dictionaries (CIF) in which higher-order parsing might be necessary. Thus, for each format, you'd need a specific test which will be defined by that format. Second, and this happens all the time, many application writers will produce files that are nearly properly formatted--read incorrectly formatted--and will break a strict parser. If you're working on a large set of files, I suggest you write a scrubber that you can apply across your files to ensure they're properly formatted before use. If you're lucky, your format will come with a nicely defined BNF grammar. Good luck. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
