Apologies, accidentally clicked “send” before I was done with writing the reply… here is the link for the “Structure Analysis and Comparison” tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> I hope this helps, Elaine
On Jan 17, 2019, at 10:23 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Ahmad Khalifa, For general information of what’s in Chimera, you can look at the User’s Guide, which lists all the tools and commands with short descriptions of each: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html>
You can also search for words like “interactions” or “H-bonds” using menu: Help… Search Documentation.
Open the tools that you want to use from the Chimera Tools menu, for example:
Tools… Structure Analysis… FindHBond Tools… Structure Analysis… Find Clashes/Contacts
There are many tutorials, including “Getting Started” for new users, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> “Structure Analysis and Comparison” for examples of finding H-bonds and clashes, etc. <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2019, at 8:32 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
How to study residue-residue interactions in Chimera? How can I show the bonds of the interacting residues?
Regards.