CCL: Algorithms of bond identification
- From: "Elaine Meng" <meng~~cgl.ucsf.edu>
- Subject: CCL: Algorithms of bond identification
- Date: Tue, 9 Sep 2014 15:28:43 -0400
Sent to CCL by: "Elaine Meng" [meng()cgl.ucsf.edu]
In the case of Chimera, it becomes clearer if you look in the paper with the
Three-dimensional hydrogen-bond geometry and probability information from a
Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.
The paper figures show definitions of various angles depending on the donor and
acceptor types, and the tables list angle criteria which are either "must
be greater than the given value" or "must be within the range of
values given" for that specific combination of types. Then Chimera lets
you specify a tolerance to make the criteria looser.
As you can see there are many different cutoffs for different combinations of
types. Although I don't know specifically, I imagine some other programs use
something simpler like a single allowed angle range for D-H-A.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco