[Chimera-users] trying to process 1000 proteins via Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 21 10:07:20 PDT 2009

Hi Jian,
There is no "dock prep" command, but there are commands "addh" and  

Some other parts of Dock Prep can also be done with commands (for  
example "delete solvent"), but python scripting may be required for  
certain steps if you need them.  I cannot advise on the python part,  
perhaps others can.

For scripting to handle multiple structures, please see previous  
posts such as:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 20, 2009, at 5:51 PM, Bisn wrote:

> Hello,
> We are Chimera users trying to process 1000 proteins, e.g., add
> hydrogen and charge. We want to do this via a Chimera for DOCK
> preparation.
> I know that Chimera accepts command line, but this is not realizable
> for processing 10000 molecules. Have you any idea of the task?
> Thanks!
> Jian Chen

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