Re: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing.
Hi Mike, I guess you are on Linux with Open-Source PyMOL, right? Can you send me the xplor file that causes PyMOL to segfault? From your backtrace it looks like the problem is related to crystal symmetry information. If you want to load some format which is not yet supported by PyMOL, the easiest solution is to convert it to some already supported format on the fly and feed that to PyMOL, if possible. Cheers, Thomas Mike Marchywka wrote, On 01/02/13 17:01: I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for xplor is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering (I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- 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] which code actually executes to load axplor file? Debugstatements not executing.
Thanks but it looks like I am ok now ( aside from orignally posting this on the wrong list LOL). My python build still hangs and has problems with the list area on right but the configure/make build process works fine and I could find the problem. Generally error checking is the last thing ayone wants to do and the positions sensitive fields are a big problem to find from a segfault. I think this is the 5..0.2 open source version. In any case, I wanted to allow for input of some custom file formats and maybe integrate with some of my old code and it now looks like I can do that. Would be happy to contribute at some point if I get something that works LOL. Thanks. Date: Thu, 3 Jan 2013 12:32:01 +0100 From: thomas.hol...@schrodinger.com To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing. Hi Mike, I guess you are on Linux with Open-Source PyMOL, right? Can you send me the xplor file that causes PyMOL to segfault? From your backtrace it looks like the problem is related to crystal symmetry information. If you want to load some format which is not yet supported by PyMOL, the easiest solution is to convert it to some already supported format on the fly and feed that to PyMOL, if possible. Cheers, Thomas Mike Marchywka wrote, On 01/02/13 17:01: I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for xplor is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering (I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- 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 -- 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] apbs2 plugin failure
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
Re: [PyMOL] Atom renaming within selection
James, alter my_sele, name=CA PyMOL might act quirky after doing that, though. Cheers, -- Jason On Thu, Jan 3, 2013 at 8:37 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Pymol users! I want to rename all atoms within selection to the selected name. I've found that the renamecommand can do it but the syntax of that comand is not quite understood for me :( Could you provide me with some example ? e.g my mollecule consist of 120 carbon atoms named as the C1, C2... C120. I want to rename all atoms to CA ( the same index for all atoms). Thanks for help James -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
