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

Eric Pettersen pett at cgl.ucsf.edu
Wed Oct 21 15:59:39 PDT 2009

Hi Jian,
	In addition there is a previous post on the chimera-dev list that is  
specifically germane to your request:


Let me know if the info in that isn't enough for what you want to do.

                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Oct 21, 2009, at 10:07 AM, Elaine Meng wrote:

> Hi Jian,
> There is no "dock prep" command, but there are commands "addh" and  
> "addcharge":
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> 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:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003261.html 
> >
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003262.html 
> >
> I hope this helps,
> Elaine
> -----
> 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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