[Chimera-users] hydrogen bonds

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 22 08:51:48 PDT 2009

Hi Bala,

(1) sidechain <-> mainchain H-bonds only.
You cannot define two groups of atoms, group1 and group2, and then  
request only group1<->group2 H-bonds.  However, you can define a group  
and request only the group<->non-group H-bonds.  You would do that by  
selecting the atoms in the group, for example,
command: select @n,ca,c,o
which would select the mainchain, and then use "selRestrict cross"  
with the "findhbond" command, or if you are using the FindHBond GUI,  
choosing the option to "Only find H-bonds with exactly one end  
selected."  Actually only the N and O would make H-bonds anyway, so  
you could just select @n,o instead.

What might be the easiest is to make a copy of your structure, and in  
that copy delete everything that is not sidechain or mainchain.  For  
command: delete ~ protein
Then with the group selected and the options set as described above,  
you would only get mainchain<->sidechain H-bonds.

(2) distance and angle cutoffs.
There is no single distance or angle cutoff, there are different  
values for each combination of donor-acceptor atom types.  The cutoff  
values were taken from a publication as described here:

The values in the publication were based on very high-resolution small  
molecule structures, so typically for PDB structures more lenient  
values are used, where the tolerance values are added to the cutoffs  
taken from the publication.

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 Jul 22, 2009, at 2:52 AM, Bala subramanian wrote:

> Friends,
> I want to see the hydrogen bond between only side chains & only main  
> chain. 1) I want to know if there is any easy way to do this in  
> chimera
> 2) What is the default distance and angle used in chimera for  
> calculating the hbond. I see that distance tolerance is 0.4 and  
> angle tolerance is 20. Do these values mean default distance and  
> angle.
> Thanks,
> Bala

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