HI Ballanah, The search area is where you draw the box. So if you want to dock into a different location, draw the box so that it just goes around that location. See the "Receptor search volume options" in the Autodock Vina tool in Chimera. The help page describes this in more detail, see: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Note that the Autodock Vina tool in Chimera is not recommended for most research purposes, see the lower part of the gray box warning on the help page (the same link as above). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 24, 2024, at 9:30 AM, Ballanah Torbett via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello,
I hope this email finds you well! I had a question about using the Chimera and its AutoDock Vina interface, as I'm relatively new to using these programs. I've been able to dock substrate onto one binding site of my protein of interest, but I'd like to apply it to the other three binding sites of the tetramer as well. I wouldn't be able to work with the monomer since the active sites are formed from the interactions between the N and C termini. I have also tried saving the session as a new PDB file and docking a new substrate, but it bound to the already-occupied site. Is there a way to dock substrate onto the other sites while "ignoring" the occupied site? Thank you!
Sincerely, Ballanah Torbett 3rd Year PhD Student Gaucher Group Georgia State University <hUOX8azaxanthlabeledactivesite.py>