[Chimera-users] Hydrogen bond

Elaine Meng meng at cgl.ucsf.edu
Mon May 3 08:47:35 PDT 2021

Dear Shakkira E,
The address for asking questions is chimera-users at cgl.ucsf.edu  CC'd here.

Different programs use different methods.  Some only use distance cutoffs, whereas Chimera also uses the angles.  Some always use the same values for different donors and acceptors, whereas Chimera uses different values for different elements and functional groups.  Also the specific value of distance and angle required can be different in different programs, so there is no surprise you may get different results.

However, as you suggested, you can adjust the values in Chimera to make them looser.  They are the "Relax H-bond constraints" values shown in the FindHBond dialog.  You can see the explanation of these values by pressing Help on the dialog, or just see the same information on our website here:

Just try using larger values of these parameters.

Or, if you are using the "findhbond" command, then there are command options to set those paramaeters, "angleSlop" and "distSlop."

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

> From: shakira shukoor <shakirashukoor1993 at gmail.com>
> Subject: Hydrogen bond
> Date: May 2, 2021 at 3:09:46 PM PDT
> Dear sir
> Does chimera software have any option to set the distance and angle criteria to view the hydrogen bond. I was not able to see any hydrogen bond in my system although hydrogen bonds do exist which I have confirmed from vmd. Why is it not visible in chimera then?
> -- 
> Best Regards
> Shakkira E

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