[Chimera-users] Missing bonds

[Elaine Meng]

Hello,
As explained in the help, there are different distance and angle cutoffs for each combination of types of H-bond donor and acceptor atoms.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria> 

If you mean that you ran FindHbond and did not find them, without having your exact data, it is impossible to guess why these specific ones are not found with default parameters.  However, you can just try increasing the angle and/or distance tolerance values until they are found.  Then you will know which parameter they did not match when you used default values.

If you are using the FindHBond tool, these values are in the "Relax H-bond constraints" section.  First make sure that "Relax H-bond constraints" is turned on (checked).  Then you can edit the angstrom and degree values for the tolerance amounts. Increasing them finds more H-bonds.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

If you are using the hbonds or findhbond command, these values are specified with the "distSlop" and "angleSlop" keywords, with "relax true" also being used.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.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 Dec 6, 2022, at 12:09 PM, Naima syed via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> I have one question that when i checked the hydrogen bonds of my original and docked (control) file, 2 bonds are missing. When I checked the distance between them, it is less than 3.40 angstroms. Can you please tell me the reason why these bonds are not showing in the Chimera.
> 
> Thank you.