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