[Dock-fans] dock prep in batch mode?

Eric Pettersen pett at cgl.ucsf.edu
Thu May 24 12:52:34 PDT 2007


> I just downloaded Dock 6 and found the example surprisingly trouble
> free.  However for my application I will need to automatically
> prepare lots of enzyme and ligand files and dock them.  The only part
> of the procedure that I don't know how to automate is the Dock Prep.
> The tutorial requires clicking through a GUI.  Yes, I could just
> write scripts to remove hydrogens, rename residues, etc .. but
> hopefully I won't need to do that.  Is there a command line
> executable version of Dock Prep?

Chimera will run without a GUI if you give it the "--nogui" flag at  
startup.  The general strategy therefore is to use that flag and  
provide any structure/script files you want processed as further  
command-line arguments.  Since DockPrep is not available as a Chimera  
text command, you will have to access it via Python.  So, for  
example, the following script will DockPrep any open models:

import chimera
from DockPrep import prep
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
prep(models)
from WriteMol2 import writeMol2
writeMol2(models, "dp.mol2")

You should look at share/DockPrep/__init__.py in your Chimera  
installation to see if there are any optional arguments you want to  
give to your prep() call (in particular you may want to use H-bond  
guided hydrogen addition rather than the default steric-only addition).

If the above was in a script file named dockprep.py, you could Dock  
Prep PDB ID 1gcn with:

chimera --nogui pdb:1gcn dockprep.py

which would produce the output Mol2 file dp.mol2, which you could  
then move to some more appropriate name if necessary.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu


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