Chimerax MCP Server
chimerax-mcp
PyPI
v0.1.1
Published by mahynotch — no publish provenance, so origin is unverified, but the source is public: the repository link below is self-declared yet readable, so you can inspect the code before adopting it.
MCP server that connects AI coding tools to UCSF ChimeraX for natural-language protein editing
The grade answers one question — how safe is this server for you to adopt — so it is computed in two auditable stages. Nothing below is an opinion or an LLM's guess; every line is a real term the deterministic engine applied, and the same input always yields the same number.
1. Threat score — 100 − 0 = 100. What the published surface and source actually contain:
The deterministic scan raised no scored threat in the surface it inspected — the threat score stayed at 100. Capability observations and advisory notes are recorded but never lower it.
2. Client adoption risk — 100 − 7 = 93. Three small, subtract-only factors that reflect your risk in adopting it — a clean scan proves less on a powerful, unverified or barely-inspectable package, so the grade says so plainly:
| Points | Adoption-risk factor |
|---|---|
| −6 | capability blast radius (high) — client exposure if the model is manipulated |
| −1 | publisher verification (public source) — no provenance, but the source is public and inspectable |
Capability observations and info notes are shown under Findings but never scored.
Open any row's finding below for the file, line and evidence behind a deduction.
Findings 4
high Tool "run_script" exposes command/code executionMTC-CAP-001
Tool "run_script" appears to run shell commands or evaluate code (keyword "run_script" in tool name). Arbitrary execution driven by model input is one of the most dangerous MCP capabilities; combined with any untrusted input it becomes RCE.
Fix: Sandbox execution, allowlist commands/arguments, and never pass model output to a shell unescaped.
Location: tool run_script
high Shell/command execution in server code (chimerax_mcp/client.py)MTC-SRC-002
In the server's implementation (`chimerax_mcp/client.py:92`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.
Evidence: raX: {exe}") proc = subprocess.Popen( [exe, "--cmd", f"remotecontrol rest start port {port}"], stdou
Fix: Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.
Location: server chimerax_mcp/client.py
medium Untrusted input can drive an external actionMTC-FLOW-005
Untrusted-input tools ([save_structure]) co-exist with external-action tools ([run_script]). A prompt injection could cause unwanted external actions, though no direct sensitive-data leak path was found.
Evidence: untrusted [save_structure] → sinks [run_script]
Fix: Require confirmation for state-changing/egress actions triggered after processing untrusted content.
Location: flow save_structure → run_script
low Mutating tool "run_script" declares no destructiveHintMTC-CAP-005
Tool "run_script" can mutate/egress but declares no destructiveHint. Clients that don't default to spec-safe behavior may not prompt before running it.
Fix: Declare accurate annotations, and gate destructive tools on user confirmation regardless.
Location: tool run_script
Tools 39
Each tool and what it can reach — statically extracted from the published source.
run_scriptruns code / shellsave_structureingests untrusted inputadd_hydrogenno sensitive capabilityalign_and_rmsdno sensitive capabilityclear_labelsno sensitive capabilityclose_structureno sensitive capabilitycolor_structureno sensitive capabilitydelete_atomsno sensitive capabilityfind_contactsno sensitive capabilityget_bfactorsno sensitive capability
Show 29 more tools ↓
get_sequenceno sensitive capabilityhide_atomsno sensitive capabilityhide_surfaceno sensitive capabilityinvert_selectionno sensitive capabilitylabel_residuesno sensitive capabilitylist_modelsno sensitive capabilitymeasure_angleno sensitive capabilitymeasure_buried_areano sensitive capabilitymeasure_distanceno sensitive capabilityminimize_energyno sensitive capabilitymutate_residueno sensitive capabilityname_selectionno sensitive capabilityopen_structureno sensitive capabilityrecord_spinno sensitive capabilityreset_viewno sensitive capabilityselect_atomsno sensitive capabilityselect_chainno sensitive capabilityselect_nearno sensitive capabilityset_backgroundno sensitive capabilityshow_cartoonno sensitive capabilityshow_electrostatic_surfaceno sensitive capabilityshow_hydrophobicity_surfaceno sensitive capabilityshow_sticksno sensitive capabilityshow_surfaceno sensitive capabilityspinno sensitive capabilitystart_recordingno sensitive capabilitystop_recordingno sensitive capabilitytake_snapshotno sensitive capabilityzoom_tono sensitive capability
Toxic flows 1
Cross-tool combinations that form a data-exfiltration primitive (untrusted input → sensitive source → external sink).
What this scan could not see
- Tools were statically extracted from the published source (39 recovered), not enumerated from a running server. Tool-poisoning, Unicode-smuggling, capability and toxic-flow analysis ran on this inferred surface, but a mis-parsed registration could be missed or mis-attributed, so tool-derived findings are capped below “confirmed”. To grade the real runtime surface, scan the running server: --command "npx -y <package>".
Versions 1
Scan history per published version. The engine is deterministic — the same version always yields the same score, so a changed score means the package itself changed.
| Version | Score | Findings | Engine | Scanned |
|---|---|---|---|---|
v0.1.1 latest |
A 93/100 | 4 | 1.12.1 | 2026-07-27 |
Embed this score
Show this server's live Trust Score in your README, docs or website. The badge is served straight from the registry and updates automatically after every rescan — no API key needed. It links back to this page, so anyone who sees the grade can also read the findings behind it instead of taking a number on faith.
Verify this score yourself
The score above is reproducible: the same package version always yields the same result. Run it locally or over the free API — no account, no LLM, fully deterministic.
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