Hi Alexis, Beautiful! You and AI are in charge of making our end-of-year ChimeraX holiday card! I'm impressed Claude got the right ChimeraX commands. A user on the ChimeraX mailing list several days ago asked about how to color a structure red and said he tried many proposals from ChatGPT and none worked. (They were all using old Chimera syntax "color red #1" instead of ChimeraX "color #1 red"). My first thought is when does this fail. What if you try a more realistic use case? For example, Show me trascription factor Ntca in pdb 8h40 I'd like to see just the trascription factor bound to the DNA without the polymerase Could you show those in ribbon style without atoms Or how about I'd like to look at how fentanyl interacts with the opioid receptor, PDB 8ef5 Could you hide the G proteins? Also hide the antibody. Show the receptor as ribbon Show just one copy of the receptor Can you show the protein residues near fentanyl in stick style Can you show hydrogen bonds between fentanyl and the protein? How many are there? If the Claude MCP agent could do this I would be blown away. Regarding having the agent control the ChimeraX GUI (push buttons, use menus) when there are no equivalent commands, I think that is not too necessary with ChimeraX because almost every GUI actions has an equivalent command and those commands are echoed to the ChimeraX Log panel, so it is even pretty easy to learn the equivalent commands. Tom
On Oct 15, 2025, at 10:25 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
I mocked something up quickly. See demos below, where I'm using Cursor as the MCP client and agent with Claude 4.5 Sonnet as the LLM:
Demo 0 <https://drive.google.com/file/d/1yAhb9fV6iQHYakqz5U50wg9lEGeYIPG2/view?usp=d...> (start ChimeraX, open a pdb, color it) Demo 1 <https://drive.google.com/file/d/1fNHQX9u7uWxYMVcPFTlCLQkCO2HL_2eS/view?usp=d...> (change colors) Demo 2 <https://drive.google.com/file/d/1fy5dGjq5e9dnT68k5eZ8RtZUmRWSC-hd/view?usp=d...> (change colors again, the JA version)
Curious to hear if anyone else is working on something similar. I think getting commands to work nicely should be easy (famous last words?). Next level will be to have the agent interact directly with the GUI, check what is being displayed, and possibly click on buttons when there are no commands to perform specific tasks. There are existing MCPs that I hope will make this feasible.
Cheers, Alexis
On Wed, Oct 15, 2025 at 7:12 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Alexis,
The UCSF ChimeraX team has not looked at using ChimeraX as an AI agent or at Model Context Protocol (MCP). Your links to github repositories that have tried to hook up AI agents to ChimeraX with MCP were a surprise to me. It would be cool to see a video using an AI agent with ChimeraX.
Tom
On Oct 15, 2025, at 6:29 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi all,
I would like to use ChimeraX via an agent. Quick googling suggests I'm not the first person to think of this (here <https://github.com/chatmol/molecule-mcp>, here <https://github.com/GDAmitha/chimerax-alphafold-mcp>), but before I dive in I thought I'd check - anyone else actively working on this? Or maybe you have worked on it and hit a roadblock?
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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