Dear Shakkira E, The address for asking questions is chimera-users@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: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo...> 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." <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

From: shakira shukoor <shakirashukoor1993@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