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

Neil Bugeja neil.bugeja at gmail.com
Wed Aug 21 23:26:11 PDT 2013

Thank you very much


On 22 August 2013 02:39, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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

Neil Bugeja
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