Hi Prathvi, If you are using the ViewDock tool, see this tutorial. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> If you aren't using ViewDock, instead you can take a look at the "Structure Analysis and Comparison Tutorial" for examples of using some relevant tools: Distance measurements, H-Bonds, Contacts, etc. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> You might consider switching to using our newer program ChimeraX instead of Chimera. It has features that Chimera does not, and in my opinion, it is easier to use. We are not developing Chimera any more. See the ChimeraX tutorial: Protein-Ligand Binding Sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 29, 2023, at 11:48 PM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I used the HPEPDOCK server (http:// huanglab.phys.hust.edu.cn/hpepdock /) to dock a ligand onto a receptor and downloaded the conformation (pose) of the ligand with lowest energy.
Next I opened the receptor and ligand structure in UCSF chimera. The ligand fitted perfectly in the binding site.
Now is it possible to know which residues of the ligand are interacting with the receptor and what is the type of non-covalent interaction between them?
Thanks in advance, Prathvi