findHBonds finds all H bonds in the given models (though the donors/acceptors can be restricted). The kind of restrictions that you can specify in the hbonds command are built on top of the findHBonds call. There is another function in the FIndHBonds module that can help you here: filterHBondsBySel from FindHBonds import findHBonds, filterHBondsBySel, recDistSlop, recAngleSlop allHBonds = findHBonds(chimera.selection.currentMolecules(), distSlop=recDistSlop, angleSlop=recAngleSlop) loopHBonds = filterHBondsBySel(allHBonds, loop, "cross") --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 22, 2015, at 2:47 AM, Ahir Pushpanath <ahir29@gmail.com> wrote:

Dear All, I am confused about what input I need to provide to the findHbond command in the FindHBond midas module. This is the help() on the command.

findHBonds(models, intermodel=True, intramodel=True, donors=None, acceptors=None, distSlop=0.0, angleSlop=0.0, interSubmodel=False, cacheDA=False).

For example if I want to find all H bonds between a pre-selected group of residues in loop, saved as:

loop = chimera.selection.currentAtoms() and the rest of the protein molecule, what command would I have to run? I am assuming the output(such as the one given in the findHbonds runcommand) would be saved into a variable if I provide one?

Ahir

-- Dr. Ahir Pushpanath PhD. Senior Biologist, Johnson Matthey.

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