[Chimera-users] Tutorials

[Elaine Meng]

Dear Bobby,
You’re welcome.  

We don’t have a tutorial for the Autodock Vina interface, but there is a manual page.  It should be reasonably friendly if you open the ligand and receptor as two separate models (from two separate input PDB files) and just fill in the required fields in Chimera’s Autodock Vina dialog, including drawing a box with the mouse in the main window to define a search area.

See the manual page for explanations of the fields in the dialog:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

Looking at other (non-Chimera) tutorials might be confusing because they are not describing using this interface in Chimera.  They might be useful for explaining what the advanced parameters mean, but you wouldn’t want to try to follow them step by step.  Also keep in mind that Autodock is a different program from Autodock Vina.

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 Mar 27, 2015, at 7:01 AM, Bobby Barnett <bobby.barnett at gmail.com> wrote:

> Dear Elaine,
> 
> I meant to thank you earlier for the many tutorials you provided, but I got distracted.
> 
> I did have another question and i will post it on the regular way if it is needed, but is there a tutorial using the Autodock Vina under the tools Surface Binding Analysis option?  I have tried several times to perform this with one of the autodock tutorials and can't get it to work under chimera.
> 
> Thanks again for your help.  I really appreciate all of the tutorials and the videos that you and your group provide.
> 
> Bobby Barnett, semi-retired crystallographer
>