[PyMOL] AutoDock plugin

Dear PyMol users! I've forced with the problem of the installation of AutoDock plugin pymoawiki.org/index.php/Autodock_plugin in recent pymol version. I've tried to install it manually from the downloaded py script but at the starting of pymol below error has bbeen appeared Unable to initialize

Re: [PyMOL] AutoDock plugin

Hi James, is it recent version of PyMOL, or recent version of Windows which makes trouble? On Windows, the plugin tries to write to the PyMOL installation folder, which fails if you don't have write permissions there. This needs to be fixed, the plugin should write to the users folder also on W

Re: [PyMOL] AutoDock plugin

Thomas, Thanks for suggestions. 1)I have installed Numpy. 2) File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 260, in parse exec(layer.com2+"\n",self.pymol_names,self.pymol_names) File "", line 1, in File "/usr/share/pyshared/pmg_tk/startup/autodock_plugin.py", line 62, i

[PyMOL] Working with the pdb ensemble

Dear PyMol users! I'd be thankfull if you provide me with the easliest way how I could save selection to the separate pdbs. For example I've loaded 10 pdbs of the receptor and selected from in each 10 ligands. This selection is defined in one object (extracted or coppied from sele). How I could sa

[PyMOL] Capture PyMOL Output When Launched From Python

Is it possible to capture the output stream from PyMOL when it is launched from a Python script with... import os, __main__ os.environ['PYMOL_PATH'] = "C:\Python27\PyMOL" __main__.pymol_argv=["pymol", "-qx"] import pymol pymol.finish_launching() I see that an IDE can do this. Is there a way for

Re: [PyMOL] Working with the pdb ensemble

Hi James - If I understand you correctly, you just need to give a selection argument to the save command. save ligand1.pdb, sele1 save ligand2.pdb, sele2 etc... See http://pymolwiki.org/index.php/Save for more info. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 5

Re: [PyMOL] Working with the pdb ensemble

Hi Jared, The issue is that the all ligands are copied in one sele (and than extracted to one object). Consequently I'd like to split it to separate objects as the lig1.pdb lig2.pdb etc James 2013/12/7 Sampson, Jared > Hi James - If I understand you correctly, you just need to give a > sele