[Chimera-users] FindHBond

Greg Friedland GDFriedland at lbl.gov
Mon Dec 14 16:32:41 PST 2009

I'm new to Chimera and just discovered the FindHBond tool. This tool 
seems very useful, but unfortunately it draws hbonds between the heavy 
atoms even when I have hydrogens added. Is there a way to configure this 
behavior? I'd like the hydrogen bonds to be drawn between the hydrogen 
and the acceptor atom. It looks rather strange now, especially for the 
hbonds with relaxed constraints that deviate significantly from the 
angle made by the hydrogen.  See the attached tiff for an example.

Also, I'm curious what cutoffs are used. I looked at 
but I was hoping for more details. I.e what numbers from the paper are 
used for the proton-acceptor distances, donor-proton-acceptor angle and 
the corresponding dihedral angle.


Greg Friedland
Joint BioEnergy Instute
Sandia National Lab
Formerly of Tanja Kortemme's lab at UCSF

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