[Chimera-users] HBond on every frames of a large trajectory

Eric Pettersen pett at cgl.ucsf.edu
Tue Apr 26 14:03:35 PDT 2016

> On Apr 26, 2016, at 11:30 AM, Jérémie KNOOPS [531802] <Jeremie.KNOOPS at umons.ac.be> wrote:
> 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 Pettersen
	UCSF Computer Graphics Lab

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160426/a0078aae/attachment.html>

More information about the Chimera-users mailing list