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

NOOR GREWAL noor.grewal at berkeley.edu
Wed Oct 18 02:28:28 PDT 2017


Thank you Elaine! I will look into UCSF DOCK instead.

On Tue, Oct 17, 2017 at 9:15 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>


-- 
*Jagnoor Grewal *
UC Berkeley | Class of 2017
Mobile: (323).813.6667
Email: noor.grewal at berkeley.edu
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