[chimerax-users] From Arun: Request for information

[Elaine Meng]

Dear Arun,

ChimeraX (and Chimera) do not calculate binding energies, sorry.

ChimeraX is in early development and doesn’t yet have many features for identifying interacting residues, other than just looking at the structure yourself and seeing what is nearby.  If you want to try Chimera, there are FindHBond and Find Contacts tools, and there are examples of using these tools in the “Structure Analysis and Comparison” tutorial.

Chimera tutorials:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
Structure Analyais and Comparison tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
Chimera download (scroll down to the tables):
<http://www.rbvi.ucsf.edu/chimera/download.html>

If you want to see what features ChimeraX has currently, one way is to scan through the User Guide index:
<http://rbvi.ucsf.edu/chimerax/docs/user/index.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 23, 2017, at 3:39 AM, Arun Prasad Chopra <arun.chopra.hcst at sgei.org> wrote:
> 
> Dear Sir,
> I was using Chimerax software to identify the residues (aminoacids and nucleotide) that are interacting and also if we can know the binding energy of this transcription factor with DNA motif.  I would be thankful for helping me identifying the residues. The PDB file is enclosed
> Thanks and Best Regards
> Arun