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From: Alex Gawronski <alex.gawronski@gmail.com> Date: August 4, 2009 1:28:42 PM PDT To: meng@cgl.ucsf.edu Subject: Re: [Chimera-users] Minimize

Hello again,

Is there a way to run Dock Prep, without GUI, from a script or command line? I tried 'start Dock Prep' with the headless linux version and it gave me a "ImportError: No module named Togl".

Thanks, Alex

You have to use a Python script in Chimera. Something along the lines of: from chimera import openModels, Molecule, runCommand from DockPrep import prep prep(openModels.list(modelTypes=[Molecule])) runCommand("write out.pdb") which you would then use in Chimera in a fashion similar to this: chimera --nogui structure001.pdb script.py mv out.pdb processed/structure001.pdb There are keyword arguments to the prep() function for changing it's behavior in the same fashion as the check buttons do in the DockPrep graphical interface. If you're familiar with Python you could modify the script to loop through your files directly in one instance of Chimera rather than calling Chimera once for each file. --Eric