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Pellaeon and the mcp command

In short. ChimeraX's built-in mcp command lets an assistant you already use, such as Claude Desktop or Cursor, send commands into ChimeraX. Pellaeon puts the assistant inside ChimeraX, with any model including free and local ones, guard rails, and analysis tools. Pellaeon's tools are ChimeraX commands, so an assistant on mcp can call them too.

Side by side

ChimeraX's mcp command
An assistant outside ChimeraXClaude Desktop, Cursor or VS Code Copilot. Its own model, its own account.
MCP bridge processA Python program the assistant starts. Speaks MCP to the assistant, HTTP to ChimeraX.
ChimeraX REST server`mcp start` opens a port. Commands arrive as text, the log comes back as text.
Toolsrun_command, list_models, get_shown, get_model_info, get_chain_info, command docs, atom-spec guide.
Runs and reportsWhatever the assistant sends runs. Retries and safety are the assistant's job.
Pellaeon
A panel inside ChimeraXA floating or docked panel next to the 3D view. A ChatGPT account, Ollama on your PC, or Mistral, Gemini, Claude, OpenAI keys.
In-processNo bridge, no port. Reads what is open and selected, the log, errors, and your loaded tables.
ContextYour ChimeraX version's docs indexed locally, 147 workflows, 58 recipes, known model mistakes.
Toolsrun commands, state, docs, UniProt, 3D-Beacons structure lists, ClinVar, AlphaMissense, ConSurf, tables, contacts, tidy labels, figures with provenance.
Checks and gatesErrors go back with the real syntax for a bounded retry. Close, delete, save and scripts stop for an OK card.
pellaeon tool ... commandsPellaeon's analysis tools are ChimeraX commands too, so an assistant on the mcp bridge, a .cxc script or the command line can call them without any chat: pellaeon tool contacts #1 #2, pellaeon tool annotate #1 P07550 variant, pellaeon tool fetch alphamissense P07550.
ChimeraX's mcp command
An assistant outside ChimeraXClaude Desktop, Cursor or VS Code Copilot. Its own model, its own account.
MCP bridge processA Python program the assistant starts. Speaks MCP to the assistant, HTTP to ChimeraX.
ChimeraX REST server`mcp start` opens a port. Commands arrive as text, the log comes back as text.
Toolsrun_command, list_models, get_shown, get_model_info, get_chain_info, command docs, atom-spec guide.
Runs and reportsWhatever the assistant sends runs. Retries and safety are the assistant's job.
Pellaeon
A panel inside ChimeraXA floating or docked panel next to the 3D view. A ChatGPT account, Ollama on your PC, or Mistral, Gemini, Claude, OpenAI keys.
In-processNo bridge, no port. Reads what is open and selected, the log, errors, and your loaded tables.
ContextYour ChimeraX version's docs indexed locally, 147 workflows, 58 recipes, known model mistakes.
Toolsrun commands, state, docs, UniProt, 3D-Beacons structure lists, ClinVar, AlphaMissense, ConSurf, tables, contacts, tidy labels, figures with provenance.
Checks and gatesErrors go back with the real syntax for a bounded retry. Close, delete, save and scripts stop for an OK card.
pellaeon tool ... commandsPellaeon's analysis tools are ChimeraX commands too, so an assistant on the mcp bridge, a .cxc script or the command line can call them without any chat: pellaeon tool contacts #1 #2, pellaeon tool annotate #1 P07550 variant, pellaeon tool fetch alphamissense P07550.

Which one

  • You live in Claude Desktop, Cursor or VS Code and want to steer ChimeraX from there: use mcp. It is built in, needs an MCP client (Claude Desktop, Cursor or Copilot, with their own accounts), and Claude Desktop runs on Mac and Windows only.
  • You want the conversation next to the 3D view, a free or local model, confirmation before anything destructive, and the analysis below: use Pellaeon.
  • Both at once works; they do not share keys, chats or settings.

Use both: Pellaeon's tools as commands

Anything that can run a ChimeraX command can run these, including the mcp bridge's run_command, a .cxc script and chimerax --nogui. No chat, no model, no key. The summary and full result go to the Log, which is what mcp returns to the assistant.

  • pellaeon tool contacts #1 #2 chain A: lost and gained contacts, drawn red and green
  • pellaeon tool compare #1 #2: superpose and color by residue displacement
  • pellaeon tool annotate #1 P07550 variant: ClinVar variants; or a UniProt feature such as transmembrane, domain, binding
  • pellaeon tool fetch alphamissense P07550: AlphaMissense per position; fetch conservation 1UBQ chain A for ConSurf
  • pellaeon tool table ~/scores.csv column hydropathy: your residue table, colored with a key
  • pellaeon tool tidy: rearrange overlapping labels
  • pellaeon tool explain #1/A:87: why this residue has its color
  • pellaeon tool list: all of the above; usage pellaeon tool contacts shows the arguments

Needs Pellaeon 0.2.1 or newer (install). The mcp command is in ChimeraX releases from December 2025 on; usage mcp tells you if yours has it, and its documentation covers the setup.