Re: [PyMOL] Autodock/Vina Pymol Plugin Windows problem
On 8 Jan 2010, at 09:51, Daniel Seeliger wrote: > > Btw, did anyone get it to run on windows or mac? If yes, it would be nice if > you drop me a mail with some info about your system (operating system, > program > version, how is pymol installed). Hi Daniel, The plug-in works great on a Mac (snow leopard; 10.6.2) with PyMOLX11hybrid 1.2r2 and MGLTools 1.5.4. Though, I had to change the first line of the scripts in "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24" so that the scripts called by the plug-in get the correct python environment parameters: "#!/usr/bin/env python" changed to "#!/usr/bin/env/Library/MGLTools/1.5.4/bin/pythonsh" Multiple errors will occur without this change. -- Florian-- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-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] Autodock/Vina Pymol Plugin Windows problem
Hi Jed, sorry for the late reply. The plugin so far doesn't work properly on windows and mac (at least that's what users report. I don't have a windows PyMOL to test it). Could you send me your input files? I'd like to test it on linux to see if there's a problem with the files or something else. Btw, did anyone get it to run on windows or mac? If yes, it would be nice if you drop me a mail with some info about your system (operating system, program version, how is pymol installed). Thanks, Daniel On Thursday 07 January 2010 04:49:11 pm Jed Goldstone wrote: > I can't seem to get the autodock Pymol plugin to work correctly in > Windows (XP). I think it's a bug somewhere. > I'm using the latest version of autodock grid and dock, and MGL Tools > 1.5.4 on Windows XP with Python25, and PyMol 1.2r1 > > I've emailed the author, Daniel Seeliger, but haven't gotten a reply. > Has any had experience with this? > > I'm getting at least 2 different errors: > first, in setting up a receptor. When I click on the PyMOL Selection and > "Generate Receptor" I get the following error: > > "Batch: C:\Program Files\MGLTools > 1.5.4\MGLToolsPckgs\AutoDockTools\Utilities24\prepare_receptor4.py -r > C:\Program Files\PyMOL\.ADplugin\receptor.dr1a.pdb -o > receptor.dr1a.pdbqt -A checkhydrogens > '{' is not recognized as an internal or external command, > operable program or batch file." > > second, if I "Select as Flexible" in the Autodock plugin a PyMol > selection, I get the following Pymol error in background function, > > Error: 1 > Exception in Tk callback > Function: > (type: 'instancemethod'>) > Args: () > Traceback (innermost last): > File "C:\Program Files\PyMOL/modules\Pmw\Pmw_1_3\lib\PmwBase.py", line > 1747, in __call__ >return apply(self.func, args) > File "C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py", line > 1800, in select_flexible_residues >receptor_object = self.receptor_dic[rec] > : '' > > > Jed > -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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] Autodock/Vina Pymol Plugin Windows problem
I can't seem to get the autodock Pymol plugin to work correctly in Windows (XP). I think it's a bug somewhere. I'm using the latest version of autodock grid and dock, and MGL Tools 1.5.4 on Windows XP with Python25, and PyMol 1.2r1 I've emailed the author, Daniel Seeliger, but haven't gotten a reply. Has any had experience with this? I'm getting at least 2 different errors: first, in setting up a receptor. When I click on the PyMOL Selection and "Generate Receptor" I get the following error: "Batch: C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\AutoDockTools\Utilities24\prepare_receptor4.py -r C:\Program Files\PyMOL\.ADplugin\receptor.dr1a.pdb -o receptor.dr1a.pdbqt -A checkhydrogens '{' is not recognized as an internal or external command, operable program or batch file." second, if I "Select as Flexible" in the Autodock plugin a PyMol selection, I get the following Pymol error in background function, Error: 1 Exception in Tk callback Function: > (type: ) Args: () Traceback (innermost last): File "C:\Program Files\PyMOL/modules\Pmw\Pmw_1_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py", line 1800, in select_flexible_residues receptor_object = self.receptor_dic[rec] : '' Jed -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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