[Chimera-users] Need help performing a high throughput screen using Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 17 09:15:33 PDT 2017


Hi Noor,
Chimera is not the right program for what you want to do.   Chimera only has a graphical interface to run a very small amount of docking (not very much sampling) for one ligand at a time, and this is not done within the program itself but using a web service run by another group.  So you cannot adjust the options to do more sampling or search a large database of multiple ligands.

You should use a docking program instead, for example, UCSF DOCK.  You can use Chimera to prepare the structures before the docking and to look at the results afterward, but the docking itself would be done with this separate program. You can download UCSF DOCK to run on your own computer; their website also has tutorials:
<http://dock.compbio.ucsf.edu/>

There is also a DOCK Blaster web service that runs the program for you
<http://blaster.docking.org/>

There are actually several different docking programs you could use, but it’s beyond the scope of this mailing list to try to summarize the field.  A few different ones are listed as the types of docking output that Chimera can read (to show results in its ViewDock tool):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 17, 2017, at 1:28 AM, NOOR GREWAL <noor.grewal at berkeley.edu> wrote:
> 
> Hello, 
> I am an undergraduate student at UC Berkeley. I want to use UCSF Chimera as a part of my research project. How can I run multiple (~20,000 ligands) ligand-docking experiments in parallel using Chimera? I have a Mac OSX Sierra and I am trying to use the command line/terminal for this. I am unable to find documentation and tutorials that can help me. I am very new to this. Could you please guide me on how to best navigate this process? 
> Thanks. 
> Best, 
> Noor 




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