10 actions in 3 pieces of software · ranked by words, meaning and measured trust · 652 ms

1. 1pymolverified and signedpassport

   skillgoogle-deepmind/science-skillsrecord

   • pymol

     Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or ana

2. 2pymol-mcpfound in code, not yet checkedno passport yet

   MCP serverubcd-ibfg/pymol-mcp

   • pymol_reinitialize

     Reset the entire PyMOL session to a clean state, discarding all loaded objects and settings.

   • pymol_run_python

     Execute arbitrary Python code inside the PyMOL session -- `cmd` is bound, so this can do anything the typed tools can plus custom numpy/iterate logic. ONLY REGISTERED because the server was started with --allow-python-exec: this is full code execution on the host machine as the user running the serv

   • pymol_run_command

     Run any PyMOL command not covered by a dedicated tool. Covers the long tail of PyMOL's command set (map operations, dss, sculpting, symmetry, etc.). Prefer a dedicated tool when one exists -- it gives you validated inputs and structured output instead of raw text.

   • pymol_set

     Change a PyMOL setting, globally or scoped to one object/selection. See pymol.org's Setting reference for the full list of names.

3. 3agentic-pymolfound in code, not yet checkedno passport yet

   MCP serverarcadia-science/agentic-pymol

   • render

     Render the current view to a PNG.

   • alter

     Modify atom attributes from a Python expression evaluated once per atom. Mirror of iterate but with assignment.

   • save

     Save a selection to disk. Format is detected from the extension if not given.

   • fetch

     Fetch a structure from RCSB and load it. Synchronous (async_=0).

   • get_coords

     Return Nx3 atom coordinates as a list of [x, y, z]. Returns [] for an empty selection — PyMOL's `cmd.get_coords` returns None in that case.