[chimerax-users] hbonds and the number of detected interactions

[Enrico Martinez]

Dear ChimeraX users!
I have a question regarding calculations of the hydrogen bonds and its
visualisation using hbonds. Here is my command:
hbonds #1 & ligand reveal true log true radius 0.06 dashes 6 color
turquoise distSlop 0.4 angleSlop 20 intraRes false

So I ignore intraRes (since the ligand is also present in the #1) and
calculate hydrogen bonds using default parameters.

1) How can I modify geometric criteria for the calculations (is this
distSlop / angleSlop) to increase the distance for the consideration
of potential h-bonds ?  In particular as you may see on the attached
image the bond between the side-chain of the Glu166 and NH of the
ligand is absent (I've just checked the same structure using py*ol and
it could detect this contact).
2) In the case of another ligand, I could visualize two h-bonds
provided by two hydrogens of the side chain of the Gln189 (same
residue) with two different oxygens of the ligand. Is this correct?
Many thanks for the tips!
Yours sincerely
Enrico
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