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
type 'exceptions.KeyError' Exception in Tk callback
Function: bound method Autodock.select_flexible_residues of
pmg_tk.startup.autodock.Autodock instance at 0x10941580 (type: 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]
type 'exceptions.KeyError': ''
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
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[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
type 'exceptions.KeyError' Exception in Tk callback
Function: bound method Autodock.select_flexible_residues of
pmg_tk.startup.autodock.Autodock instance at 0x10941580 (type: 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]
type 'exceptions.KeyError': ''
Jed
--
Jed Goldstone
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
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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
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