[Chimera-users] Hydrogen bond cut off

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 7 16:11:26 PDT 2011

Hi Simon,
There is no single cutoff distance and angle.  If it were that simple, we would of course put the values in the manual page. Instead, there are many different criteria depending on the atom type of the H-bond donor and the atom type of the H-bond acceptor. The various values are listed in some tables of Mills reference, which I will attempt to locate and send you in a subsequent message.

Our reasoning for using these multiple values: because the high-resolution crystal structure data showed different distributions of distances and angles for H-bonds depending on the atom types involved, we can perform a higher-quality H-bond detection by similarly using the cutoff values most appropriate for the types of atoms being examined.


"There are many different sets of geometric criteria, corresponding to the many different donor-acceptor combinations (see Tables 5-8 in the reference). There is an upper bound on distance and one or more angular range criteria for each category of H-bond."

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 7, 2011, at 4:00 PM, Simon Sham wrote:

> Hi,
> First, I don't have access to the reference by JE Mills in Journal of Comp. Aided Design 1996.
> Secondly, can someone please tell me that in chimera is the cut off distance between the donor and acceptor atoms 3.5 angstroms and cut off angle 35 degrees?
> Thanks for your help in advance.
> Simon  

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