[Chimera-users] Highlighting the H bonds during simulation

Elaine Meng meng at cgl.ucsf.edu
Tue May 31 15:51:01 PDT 2016

Hi Natesh,
The exact commands would depend on your system (how to specify the ligand), but I can at least give you an example.  If “select ligand” selects only your ligand, it could be something like

chain @ca
~disp solvent
select ligand; hb selRestrict cross line 2 color yellow reveal true; ~select

If “select ligand” doesn’t select only your ligand of interest, you would need to instead use its residue number(s) or names to select it.

Basically this uses the “selRestrict” option of “hbonds”  to limit the detection to just H-bonds with one end in the selected ligand.  I put the select and unselect commands in the same line (separated with semicolons) so that the green selection outline will not show up.  Putting the commands in the same line separated by semicolons hides the intermediate states.  

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 May 31, 2016, at 2:21 AM, Natesh Singh <a1468984 at unet.univie.ac.at> wrote:
> Dear Sir,
> How could I highlight the formation and breakdown of Hbonds with the ligand to that of residues during the md simulation. I tried using the script (per-frame commands)
> chain @ca
> ~disp solvent
> hb line 2 color yellow reveal true
> Using this command, highlights all Hbonds in the system during the simulation, but I would like to see only Hbond interactions with ligand to that of nearby residues. How could I do this? what would be the appropriate per-frame script?
> Looking forward for the guidance.
> Best regards,
> Natesh
> Uni.Wien

More information about the Chimera-users mailing list