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 (start ChimeraX, open a pdb, color it)

Demo 1 (change colors)

Demo 2 (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> 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> 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, here), 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
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