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 On Thu, Feb 26, 2015 at 1:09 PM, Elaine Meng <meng@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@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