[Chimera-users] question about report of hydrogen bonds that Chimera produces
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.
> 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
(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
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
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 C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
More information about the Chimera-users