[Chimera-users] Query (how to find H-bonds)

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 28 13:54:38 PDT 2017

Dear Dr. Selvaraj,
I CC’d chimera-users at cgl.ucsf.edu (this is the best address for Chimera questions).

I don’t know where you are seeing “no H-bonds” because I didn’t have that problem. If I start Chimera, open your two files, and choose menu: Tools… Surface/Binding Analysis… FindHBond, and click “Apply” on that dialog (or “OK” which is the same, except it also makes the dialog disappear), it says in the Reply Log that there are 629 H-bonds found. (open Reply Log from Favorites menu)  Many orange lines are drawn on the structure to show the H-bonds. 

If you want to label the H-bonds with distance, check the “Label H-bond with distance” option before clicking Apply.

 If you want to make sure all the H-bonds are shown, check the option “If endpoint atom hidden, show endpoint residue”.

If you only want the H-bonds between the two proteins, not the ones within each protein,  check the “inter-model” option near the top right of the dialog.  With that option, Reply Log says that 312 hydrogen bonds are found.

There are also options to write all the information (atom names, distances etc.) to the Log and/or to an output text file.

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

> On Sep 27, 2017, at 5:52 PM, Gurudeeban Selvaraj <gurudeeb99 at qq.com> wrote:
> Dear Support Team,
>           Thanks for the academic free of Chimera. I have a doubt, how can I visualize H-bonding interactions of docked structure of protein-protein interaction. I used FireDock for docking studies. While running on FindHbond on structure/binding tool it says no H-bonds, but i click both shows something.....How can i see protein-protein interacting HBond and label it?
> For the reference, I enclosed two files.
> Thanks in advance!
> ------------------
> Sincerely
> Dr. Gurudeeban Selvaraj, Ph.D.
> Postdoctoral Researcher

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