CCL: Algorithms of bond identification

 Sent to CCL by: "Elaine  Meng" []
 Hi Grigoriy,
 Some programs just use a simple single distance cutoff between donor and
 acceptor heavy atoms, while others also use an angle cutoff.  Probably you would
 have to look at the manual of each program to find the details.
 I work on UCSF Chimera, and its method is relatively complicated in that there
 are many different cutoffs:  it uses different distance and angle cutoffs
 depending on the atom types of the donor and acceptor.  It uses certain values
 for each combination of types as observed in a set of high-resolution small
 molecule crystal structures.  Then to those values, the user can specify an
 extra distance tolerance and angle tolerance, since the criteria from the survey
 are very strict.  Details here:
 Elaine C. Meng, Ph.D.
 UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
 Department of Pharmaceutical Chemistry
 University of California, San Francisco