[Chimera-users] rotamers, contacts, H-bonds

[Elaine Meng]

Hello Maryam,
This sounds like a chimera-users question (chimera-dev is more about programming), so I CC'd that address.  

You can use Distance measurements, Find Contacts/Clashes and/or FindHBond to look at the interactions of the residue.  See menu under Tools.. Structure Analysis, and instructions:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

For looking at rotamers of amino acids, both same type as native (no mutation) or different type (mutation) you could use the Rotamers tool (in menu under Tools… Structure Editing).  The rotamers list also connects to finding contacts and Hbonds through its Columns menu, see "evaluation" in the Rotamers manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>

For examples of measuring distances, identifying contacts and H-bonds, and using Rotamers, I recommend you try the "Structure Analysis and Comparison" tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

Regards,
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 May 28, 2014, at 2:05 AM, "maryam.khoshnejat" <maryam.khoshnejat at modares.ac.ir> wrote:

> hello
> could you help me?
> i should model specific mutant residue of protein . i have PDB file and rotamer of mutant residue
> how can i find coordination of mutant residue based on backbone and CB coordination of native residue , rotamer and atom bonding distance
> i need a code for finding coordination of mutant residue
> regards