I have an additional question : what's the way to restrict the residues to search for hbond donors & acceptors with python commands?
I overlooked this question on my first read. You do it by specifying the donors/acceptors keywords in the findHBonds() call. The simplest way to do that is to select the residues you want to restrict the search to, by whatever means you find convenient, and then in the script:
from chimera.selection import currentAtoms
donors = acceptors = currentAtoms()
…and the end of the FindHBonds call in the script would be modified to look like:
…, cacheDA=True, donors=donors, acceptors=acceptors))
—Eric
Eric Pettersen
UCSF Computer Graphics Lab