[Chimera-users] question about Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 22 11:00:11 PDT 2009

Dear Wu Xue,
There are several different distance and angle cutoffs that depend on  
the donor and acceptor atom types.  For example, the distance and  
angle cutoffs for finding a H-bond donated from hydroxyl -OH to  
carbonyl =O will be different than from amine -NH3 to carbonyl =O.   
The cutoff values are taken from tables in this paper:

     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.

As discussed in the FindHBond documentation,

the criteria in this paper were based on very high resolution crystal  
structures of small molecules.  Typically the structures in the PDB  
are not so high resolution and so the criteria are relaxed.  For  
example, if a strict criterion from the paper is 2.8 Angstroms  
cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms.   
We set the default relaxation amounts to what we felt gives  
reasonable results on most PDB structures.  However, we made them  
user-adjustable so that if you don't like them, you can change the  
values to whatever you want.

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

On Sep 22, 2009, at 4:18 AM, 吴雪 wrote:

> Dear colleague:
>     I have  a question about the "find hydrongen bond" in Chimera.  
> The dumb relax constraints in Chimera are "0.04 nm" and "20 degree".
>    I don't understand the meaning of the parameter. 20 degree may  
> means the angle bias the line,but I can't figure out what is the  
> 0.04nm.
> The cutoff of the hydrogen is 0.4nm, and the angle is about 90  
> degree or some other parameters depending on the strength of the  
> hydrogen bond.
>   If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds  
> are found. I don't know the criteria. Can you give me some advice  
> so that I can follow your instruction?
>    Sincerly Yours
>    WU Xue

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