[Chimera-users] Tutorials

Elaine Meng meng at cgl.ucsf.edu
Sat Mar 28 15:43:53 PDT 2015


Dear Bobby,
It sounds like you need to make sure to specify an output location where you have permission to read and write files.  For example, my directory (Mac) is /Users/meng and I can specify output as /Users/meng/test (or /Users/meng/Desktop/test , etc.) to create several files with filenames that start with “test”… but of course you would need to specify a different pathname according to however your computer is set up.
Elaine

On Mar 28, 2015, at 11:25 AM, Bobby Barnett wrote:

> Dear Elaine,
> 
> Thanks for the advice about using the Autodock Vina option under Surface/Binding Analysis.  I have run this with both the web based option and the local option and get  the same error "[Errno 13] Permission denied: 'trial.receptor.pdb'"  I don't see a way around this error.  Do I need to run the program as Administrator?
> 
> Thanks again for your help.
> 
> Bobby Barnett
> 
> 
> 
> On Fri, Mar 27, 2015 at 1:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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
> >



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