[Chimera-users] Tutorials

Bobby Barnett bobby.barnett at gmail.com
Fri Mar 27 07:01:23 PDT 2015

Dear Elaine,

I meant to thank you earlier for the many tutorials you provided, but I got

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

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

On Thu, Feb 26, 2015 at 1:09 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Bobby,
> We have quite a few Chimera tutorials, but the main issue for you is
> probably whether they are suitable for undergraduates.  Maybe other
> undergraduate educators will have better suggestions or materials that they
> can send you; the tutorials that we provide do presuppose some knowledge of
> protein structure and organic chemistry, but you can take a look and see
> what you think...
> The User's Guide (included with Chimera download but also shown on our
> website) includes several tutorials, including "getting started" for
> Chimera beginners.  You can get to the copies included in your download
> from the Chimera Help menu.  The copies at our website are here, but if you
> stick with the downloaded ones (menu: Help… Tutorials) they are
> version-synchronized with the software.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
> While "getting started" may be simplest in terms of Chimera, some of the
> others in the User's Guide that are more basic in terms of the science are
> the Surface Properties image tutorial and the Structure Analysis and
> Comparison tutorial.  I usually suggest the latter for graduate students
> learning Chimera because it includes several common protein analysis tasks.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> There are also a bunch of tutorials on the website only, listed here:
> <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
> The most basic of these Chimera-wise is the expanded "getting started"
> tutorial:
> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
> 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 Feb 26, 2015, at 9:32 AM, Bobby Barnett <bobby.barnett at gmail.com>
> wrote:
> > I was wondering if anyone had interactive tutorial session(s) that can
> be used to educate a small class of undergraduate students.
> >
> > Bobby Barnett
> >
> > Department of Chemistry
> > University of Chemistry
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