Re: [PyMOL] Anaglyph colours
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 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL 1.6 pre-release announcement
This is fixed in SVN rev 4032. Cheers, Thomas Thomas Holder wrote, On 06/15/13 10:45: Hi Rob, this has not been fixed yet, I'm really sorry. We'll look into this ASAP. It only affects the open-source code, apparently we missed something when syncing with the incentive codebase. Cheers, Thomas On Jun 14, 2013, at 9:23 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hello Thomas and David, Was there any resolution of this? I've just compiled the latest version from SVN and I have the same problem opening files created under version 1.5.0. This is on Debian testing (32-bit). Cheers, Rob On Fri, 2013-04-26 19:15 EDT, David Hall li...@cowsandmilk.net wrote: Hi Thomas, I'm running into issues with color compatibility between 1.6 and earlier versions when opening pses (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: Setting-Error: type read mismatch (color) 6 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismatch (color) 664 (b) background color disparity: saved in 1.5 with black background; opens in 1.6 with a white background saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red background These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, others who would like to beta test can use devel:languages:python repo in openSUSE: https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython -David -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] APBS error
Thank you so much Troels, This solves my problem. But based on this, it seems that APBS In pymol failed to find PDB2PQR. Chen On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet tlin...@gmail.comwrote: Have a look on the earlier message on this. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html Troels Emtekær Linnet 2013/6/18 Chen Zhao chenzhaoh...@gmail.com Dear Pymol Users, I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian Wheezy machine. The initialization is successful, but when I hit set grid, I got the error message below: *error: 1 type 'exceptions.UnboundLocalError' Exception in Tk callback Function: function lambda at 0x33a6938 (type: type 'function') Args: () Traceback (innermost last): File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1075, in execute self.runPsize() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1096, in runPsize good = self.generatePqrFile() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1007, in generatePqrFile good = self._generatePdb2pqrPqrFile() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1615, in _generatePdb2pqrPqrFile if retval != 0: type 'exceptions.UnboundLocalError': local variable 'retval' referenced before assignment* Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py file, the APBS GUI in pymol is still unable to show the correct path of APBS and PDB2PQR. Thank you so much! Sincerely, Chen -- 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
[PyMOL] Problems with Pymol v 1.6.0.0
Two minor, but annoying, problems with the new version in Debian 7.0 64 bit/ #1 The pull down menus in the graphics windows refuse to remain open when clicked, unless I left click and hold. Is this normal behavior? #2. Caver 2.1.2 will not save the location of the Directory with the plug-in .jar file. The work around is rather cumbersome. -- 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] APBS error
Do you have linux or windows? Do you have PDB2PQR on your system? http://pymolwiki.org/index.php/Apbsplugin http://www.poissonboltzmann.org/pdb2pqr Troels Emtekær Linnet 2013/6/18 Chen Zhao chenzhaoh...@gmail.com Thank you so much Troels, This solves my problem. But based on this, it seems that APBS In pymol failed to find PDB2PQR. Chen On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet tlin...@gmail.comwrote: Have a look on the earlier message on this. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html Troels Emtekær Linnet 2013/6/18 Chen Zhao chenzhaoh...@gmail.com Dear Pymol Users, I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian Wheezy machine. The initialization is successful, but when I hit set grid, I got the error message below: *error: 1 type 'exceptions.UnboundLocalError' Exception in Tk callback Function: function lambda at 0x33a6938 (type: type 'function') Args: () Traceback (innermost last): File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1075, in execute self.runPsize() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1096, in runPsize good = self.generatePqrFile() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1007, in generatePqrFile good = self._generatePdb2pqrPqrFile() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1615, in _generatePdb2pqrPqrFile if retval != 0: type 'exceptions.UnboundLocalError': local variable 'retval' referenced before assignment* Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py file, the APBS GUI in pymol is still unable to show the correct path of APBS and PDB2PQR. Thank you so much! Sincerely, Chen -- 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
Re: [PyMOL] APBS error
Hi Chen. If you are up for it, pdb2pqr exist in the Pymol-script repo. http://pymolwiki.org/index.php/Git I have made a automatic compile script. See here: http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script That should fix it for you. Try to look it through, and just write if you have problems. Troels Emtekær Linnet 2013/6/18 Chen Zhao chenzhaoh...@gmail.com I am using Debian linux and I installed PDB2PQR with path specified in pymol APBS GUI. However, it seems that there are some problems in python, although I don't understand because I am not a programmer. I will try to run from command line instead. Thank you! Chen On Tue, Jun 18, 2013 at 11:08 AM, Troels Emtekær Linnet tlin...@gmail.com wrote: Do you have linux or windows? Do you have PDB2PQR on your system? http://pymolwiki.org/index.php/Apbsplugin http://www.poissonboltzmann.org/pdb2pqr Troels Emtekær Linnet 2013/6/18 Chen Zhao chenzhaoh...@gmail.com Thank you so much Troels, This solves my problem. But based on this, it seems that APBS In pymol failed to find PDB2PQR. Chen On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet tlin...@gmail.com wrote: Have a look on the earlier message on this. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html Troels Emtekær Linnet 2013/6/18 Chen Zhao chenzhaoh...@gmail.com Dear Pymol Users, I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian Wheezy machine. The initialization is successful, but when I hit set grid, I got the error message below: *error: 1 type 'exceptions.UnboundLocalError' Exception in Tk callback Function: function lambda at 0x33a6938 (type: type 'function') Args: () Traceback (innermost last): File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1075, in execute self.runPsize() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1096, in runPsize good = self.generatePqrFile() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1007, in generatePqrFile good = self._generatePdb2pqrPqrFile() File /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1615, in _generatePdb2pqrPqrFile if retval != 0: type 'exceptions.UnboundLocalError': local variable 'retval' referenced before assignment* Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py file, the APBS GUI in pymol is still unable to show the correct path of APBS and PDB2PQR. Thank you so much! Sincerely, Chen -- 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
[PyMOL] Leapmotion ?
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
Re: [PyMOL] Leapmotion ?
That looks so cool. Please make a video/blog of the outcome! /Troels Troels Emtekær Linnet 2013/6/19 Aurélien Grosdidier aurelien.grosdid...@gmail.com: 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 -- 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 javascript:; ) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
