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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/usageconventions.html> 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
On May 31, 2016, at 2:21 AM, Natesh Singh <a1468984@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