How to study residue-residue interactions in Chimera?
How to study residue-residue interactions in Chimera? How can I show the bonds of the interacting residues? Regards.
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. or
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.
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Ahmad Khalifa -
Elaine Meng