[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])
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 Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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