From owner-chemistry[ AT ]ccl.net Tue Sep 9 15:30:00 2014 From: "Elaine Meng meng+/-cgl.ucsf.edu" To: CCL Subject: CCL: Algorithms of bond identification Message-Id: <-50485-140909152846-25990-Fqk45eP5S3z5OIOyLjKgOw++server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 9 Sep 2014 15:28:43 -0400 Sent to CCL by: "Elaine Meng" [meng()cgl.ucsf.edu] Hi Grigoriy, In the case of Chimera, it becomes clearer if you look in the paper with the H-bonding criteria: Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. 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 ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco