MCP server in WSL can't connect to PyMOL running on Windows

[vpanagiotou531]

hello,

i am using windows 11 and pymol, and i also have ubuntu 22.04 installed in my windows 11 laptop via wsl

i tried to install agentic pymol through wsl, while having pymol opened through windows 11 and claude opened through wsl and vscode, and i did not achieve to execute agentic pymol although i did all of the steps of the video procedure

the error printed was this (inside claude CLI) -> ● PyMOL isn't reachable — the MCP plugin can't connect to PyMOL at the expected address. Please make sure:

1. PyMOL is running on your machine.
2. The MCP plugin is started inside PyMOL — typically by running the plugin script or via the Plugin menu if it's installed.

how can i fix this installation issue? i must use windows 11 laptop for this task and i dont have a linux or mac laptop as a 2nd-choice laptop

thank you

[ekiefl]

The general fix would be to get PyMOL and the MCP server onto the same network — either by enabling WSL2 mirrored networking (note: may also require a Windows Firewall rule for the inbound connection), or, more reliably, by running PyMOL inside WSL via WSLg so everything shares one loopback. Both are standard WSL setup with resources available. This isn't an Agentic PyMOL issue per se, it's a networking failure that arises when you run an operating system inside an operating system.

I'll keep this open in case anyone with the same setup can report their failures/successes.