Thanks so much Elaine! I managed to get it working. And apologies for posting to the wrong list. Jade On Sun, Sep 22, 2024 at 12:44 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jade, This chimera-users email address is for questions about Chimera. In the future, for questions about ChimeraX, please instead use the other address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd on this message) to avoid confusing other users.
This answer is for ChimeraX and does not apply to Chimera:
If you meant you wanted a single surface that goes around both the ligand and the protein in a single blob:
You would have to use the "surface" command with the "include" option to make a single surface around both the ligand and the protein. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options>
Then you would have to use "coulombic" command with the "surfaces" option to use the surface you already made instead of one that has the protein only. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html#charges>
Example commands for PDB file 8iyx with GPR34 receptor with antagonist bound, residue name S6R. This example assumes you want to see the potential that is from both the receptor and the ligand, on the surface that is both the receptor and the ligand.
open 8iyx surface include protein | :S6R coulombic protein | :S6R surfaces #1.2
The surface command says to make a single blob around both protein and residue S6R (the symbol between them is a vertical bar character). The coulombic command says to calculate the electrostatics using the charges of both the protein and residue S6R, and use it to color the previously made surface #1.2. You have to look in the Models panel and use the disclosure triangle to see what model number the surface has.
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 Sep 21, 2024, at 11:07 PM, jadeshi88--- via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi, New user to ChimeraX here, would really appreciate some help!
I'm trying to generate an electrostatic potential surface for a protein-ligand complex. Currently, I am using the surface/coulombic, and surface ligand/coulombic ligand commands to generate surfaces separately for the protein and ligand, and then exporting to an .obj file. However, by doing so I'm left with two separate surface meshes, and what I really want is a single surface that encapsulates both entities. Is it possible to do this?
Thanks in advance!