[Chimera-users] question about report of hydrogen bonds that Chimera produces

Elaine Meng meng at cgl.ucsf.edu
Mon May 22 15:52:50 PDT 2017


> On May 22, 2017, at 2:43 PM, Roberto Garza-Lopez <RAGL4747 at pomona.edu> wrote:
> 
> Hi Elaine, I saw your name in the chimera group in a conversation on line and I was wondering if I can ask you a very simple question.
>  
> I used FindHBond under Structure Analysis to generate the document with all the hydrogen bonds for  protein PDB# 1aac (amicyanin).  See attached.
>  
> I noticed that for some H bond distances  the report includes both  A---B  and  B---A  like in the cases below which of course have the same distance. 
>  
> <image001.png>
> <image002.png>
>  
> <image003.png>
> <image004.png>
> 
> However for other cases like the one below, I do not find the reverse, meaning   LEU 80.A O  à   VAL 43.A N.   WHY IS THAT?
>  
> VAL 43.A N LEU 80.A O no hydrogen 2.815 N/A
>  
> Thanks, 
> Roberto

Hi Roberto
(CC-ing chimera-users at cgl.ucsf.edu , recommended address for Chimera questions)

It is because the lines list H-bond donor before H-bond acceptor.  Some groups can be both donor and acceptor, but some groups (like carbonyl O) can only be acceptors, and some can only be donors.

The results include a title row which explains what the columns mean.  For example, opening 1aac and running findhbond gives:

#0, chain A: amicyanin
1aac opened

Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	#0 1aac

H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ASP 1.A N       HOH 297.A O.1   no hydrogen  3.132  N/A
ASP 1.A N       HOH 297.A O.2   no hydrogen  3.093  N/A
ASP 1.A N       HOH 297.A O.3   no hydrogen  3.360  N/A
LYS 2.A N       LEU 62.A O      no hydrogen  2.776  N/A
[… etc. …]

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






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