On May 22, 2017, at 2:43 PM, Roberto Garza-Lopez <RAGL4747@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@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