[Chimera-users] dock prep in batch mode?

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 11 16:02:41 PDT 2007

On Jun 9, 2007, at 7:52 AM, figo wrote:

>                              I have seen your solution to the dock  
> prep in batch mode (http://blur.compbio.ucsf.edu/pipermail/dock- 
> fans/2007-May/001043.html ) ,  but  when I  run the  command :  
> chimera --nogui pdb:1gcn dockprep.py ,  the chimera  want to Fetch  
> protein 1gcn from web site www.rcsb.org, I have download the  
> entire  PDB, so how can I specify the PDB path to the chimera? Thanks.

	If you have the PDB files laid out the same way that the RCSB  
distributes them (e.g. entry 1GCN is in gc/pdb1gcn.ent) then Chimera  
will automatically look in /mol/pdb and /usr/mol/pdb for them.  To  
have it look elsewhere you need to edit the file <your Chimera  
installation>/share/chimera/pdbDir and follow the reasonably simple  
instructions contained in that file.  The drawback is that you will  
need to do that edit every time you install a new Chimera.  Putting a  
better mechanism in place is on our to-do list.
	Other alternatives include putting the full path to the PDB file in  
your command, or putting all the files you need into one directory  
and using the PDB preferences (Favorites...Preferences...[change to  
PDB category]) to get Chimera to look in that directory.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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