[Chimera-users] Label hydrogen bonds

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 30 11:06:33 PDT 2018

Dear Pawan,
This is not a bug, just a question of how to do something (so we put it on this chimera-users at cgl.ucsf.edu list, which is for questions).

If you are using the FindHBond graphical tool, there is an option to “Label H-bond with distance”:

Another FindHBond option you should probably use is "If endpoint atom hidden, show endpoint residue" - this will show atoms/bonds so you can see sidechain H-bonds.  If you are only showing ribbons, it will only show the backbone H-bonds. 

If you don’t want to find ALL of the H-bonds, for example you want only to find the ones between the enzyme and the inhibitor, you should select either the enzyme or the inhibitor (for example, Ctrl-click to select part of it and then press up arrow until it is selected and outlined in green, but the other molecule is not selected) and then choose FindHBond option “only find H-bonds with exactly one end selected”

After you show the H-bonds you want, then label the H-bonded residues:
(1) show Pseudobond Panel (main menu: Tools… General Controls… Pseudobond Panel) and then in the left side choose “hydrogen bonds” and on the right side choose “select bonded”
(2) label the selected residues with main menu:  Actions… Label… residue.. [choose the type of labeling you want]

Really, it just sounds like you need to learn a little bit more about using FindHBond and Chimera.  You could try doing some tutorials, like “Getting Started”

“Structure Analysis and Comparison” (which includes finding ligand-receptor H-bonds)

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 28, 2018, at 1:03 AM, Pawan Mainkar <pawan_10549 at iari.res.in> wrote:
> Chimera Version: 1.11.2
> Description
> Respected sir,
> I am a PhD student in the discipline of Biotechnology, actually sir  i am working on Enzyme-inhibitor docking study and i did docking using Cluspro and then i want to check how much interaction by visualizing the inter molecular hydrogen bonds with proper labeling (like in structure hydrogen bond between D45-S89 with 2.3 Angstron) ,but sir am only able visualize only hydrogen bonds in Your software UCSF Chimera but am unable to label it with proper amino acid along with distance so i request you sir please tell me how to do that or provide me any video file regarding the same
> File attachment: Docking complex.docx
> <Docking complex.docx>

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