CCL: Algorithms of bond identification



 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