[Chimera-users] [chimera-dev] UCSF Chimera Help

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 21 17:39:02 PDT 2013


Dear Neil,
Chimera does not do docking except for fairly limited single-ligand calculations using an AutoDock Vina web service: you can only dock one ligand at a time and get up to 10 orientations back.  You can't search a database of ligands, for example.

The interface to the Vina web service is in the menu of Chimera version 1.7 (Jan 2013) and newer:  Tools... Surface/Binding Analysis... AutoDock Vina.  It is recommended you run other tools first to prepare the receptor before using this tool.  See the manual page for details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

However, Chimera does have a nice "ViewDock" interface for looking at the output from several docking programs that could be run outside of Chimera: DOCK, AutoDock, AutoDock Vina, Glide, GOLD, Mordor.  If the fairly simple interface mentioned above does not suffice for what you want to do, you may want to try one or more of those other programs (several are free). The ViewDock man page includes links to their websites; see the "input" section:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
There is also a ViewDock tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>

I CC'd the chimera-users list because this is more of a user question than a developer (programming) issue. 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 Aug 21, 2013, at 1:23 AM, Neil Bugeja wrote:

> Dear Sir/Madam
> 
> I am a student at the University of Malta and I am currently using your software to carry out homology modelling for my thesis.
> 
> I have a slight problem figuring out how to dock a ligand into a receptor on the program...Is this possible or do I need to install another software?
> I tried looking through the available tutorials but cannot find any so far
> 
> Thank you for your help
> 
> Regards




More information about the Chimera-users mailing list