Chimerax — the complete, unedited output of the deterministic mcptrustchecker engine v1.12.1, scanned . Every finding, capability tag and score component below is exactly what the engine produced — no AI, no post-processing.
{
"tool": {
"name": "mcptrustchecker",
"version": "1.12.1",
"methodologyVersion": "mcptrustchecker-1.12"
},
"target": {
"id": "chimerax-mcp",
"source": {
"kind": "package",
"origin": "chimerax-mcp"
},
"server": {
"name": "chimerax-mcp"
}
},
"grade": "A",
"score": {
"score": 93,
"threatScore": 100,
"grade": "A",
"band": "A",
"categorySubtotals": {
"injection": 0,
"exfiltration": 0,
"permissions": 0,
"supply-chain": 0,
"network": 0,
"hygiene": 0
},
"vector": [
{
"kind": "client",
"term": "capability-exposure",
"level": "high",
"label": "capability blast radius (high) — client exposure if the model is manipulated",
"appliedPenalty": 6
},
{
"kind": "client",
"term": "verification-discount",
"level": "repo",
"label": "publisher verification (public source) — no provenance, but the source is public and inspectable",
"appliedPenalty": 1
},
{
"kind": "client",
"term": "coverage-honesty",
"level": "source",
"label": "inspection depth (source) — how much of the target the scan could see",
"appliedPenalty": 0
}
],
"gatesFired": [],
"methodologyVersion": "mcptrustchecker-1.12"
},
"capability": {
"level": "high",
"reasons": [
"ingests untrusted external content (a prompt-injection entry point)",
"can execute shell commands or code"
],
"tags": [
"untrusted-input",
"code-exec"
]
},
"coverage": {
"level": "source",
"inputs": {
"toolSurface": true,
"implementationSource": true,
"packageMetadata": true,
"liveTransport": false
},
"caveats": [
"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>\"."
]
},
"findings": [
{
"ruleId": "MTC-CAP-001",
"title": "Tool \"run_script\" exposes command/code execution",
"category": "permissions",
"severity": "high",
"confidence": "strong",
"description": "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.",
"remediation": "Sandbox execution, allowlist commands/arguments, and never pass model output to a shell unescaped.",
"location": {
"kind": "tool",
"name": "run_script"
},
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"tags": [
"code-exec"
]
}
},
{
"ruleId": "MTC-SRC-002",
"title": "Shell/command execution in server code (chimerax_mcp/client.py)",
"category": "permissions",
"severity": "high",
"confidence": "strong",
"description": "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.",
"remediation": "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": {
"kind": "server",
"name": "chimerax_mcp/client.py"
},
"evidence": "raX: {exe}\") proc = subprocess.Popen( [exe, \"--cmd\", f\"remotecontrol rest start port {port}\"], stdou",
"owasp": "LLM05:2025 Improper Output Handling",
"data": {
"rule": "MTC-SRC-002",
"file": "chimerax_mcp/client.py",
"line": 92,
"nonRuntime": false
}
},
{
"ruleId": "MTC-FLOW-005",
"title": "Untrusted input can drive an external action",
"category": "exfiltration",
"severity": "medium",
"confidence": "strong",
"description": "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.",
"remediation": "Require confirmation for state-changing/egress actions triggered after processing untrusted content.",
"location": {
"kind": "flow",
"name": "save_structure → run_script"
},
"evidence": "untrusted [save_structure] → sinks [run_script]",
"owasp": "LLM06:2025 Excessive Agency",
"references": [],
"data": {
"untrusted": [
"save_structure"
],
"sinks": [
"run_script"
]
}
},
{
"ruleId": "MTC-CAP-005",
"title": "Mutating tool \"run_script\" declares no destructiveHint",
"category": "hygiene",
"severity": "low",
"confidence": "heuristic",
"description": "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.",
"remediation": "Declare accurate annotations, and gate destructive tools on user confirmation regardless.",
"location": {
"kind": "tool",
"name": "run_script"
},
"data": {
"tags": [
"code-exec"
]
}
},
{
"ruleId": "MTC-SUP-012",
"title": "Package has no license",
"category": "hygiene",
"severity": "info",
"confidence": "strong",
"description": "\"chimerax-mcp\" has no declared license. This is a legal/reuse concern, not a security finding.",
"location": {
"kind": "package",
"name": "chimerax-mcp"
}
}
],
"toxicFlows": [
{
"id": "flow-1",
"severity": "medium",
"confidence": "strong",
"untrustedInput": [
"save_structure"
],
"sensitiveSource": [],
"externalSink": [
"run_script"
],
"selfContained": false,
"description": "Untrusted input can drive an external action even though no sensitive source is exposed."
}
],
"capabilities": [
{
"tool": "open_structure",
"tags": [],
"reasons": {}
},
{
"tool": "close_structure",
"tags": [],
"reasons": {}
},
{
"tool": "save_structure",
"tags": [
"untrusted-input"
],
"reasons": {
"untrusted-input": [
"keyword \"download\""
]
}
},
{
"tool": "list_models",
"tags": [],
"reasons": {}
},
{
"tool": "get_sequence",
"tags": [],
"reasons": {}
},
{
"tool": "run_script",
"tags": [
"code-exec"
],
"reasons": {
"code-exec": [
"keyword \"run_script\" in tool name"
]
}
},
{
"tool": "mutate_residue",
"tags": [],
"reasons": {}
},
{
"tool": "delete_atoms",
"tags": [],
"reasons": {}
},
{
"tool": "add_hydrogen",
"tags": [],
"reasons": {}
},
{
"tool": "minimize_energy",
"tags": [],
"reasons": {}
},
{
"tool": "color_structure",
"tags": [],
"reasons": {}
},
{
"tool": "show_electrostatic_surface",
"tags": [],
"reasons": {}
},
{
"tool": "show_hydrophobicity_surface",
"tags": [],
"reasons": {}
},
{
"tool": "show_surface",
"tags": [],
"reasons": {}
},
{
"tool": "hide_surface",
"tags": [],
"reasons": {}
},
{
"tool": "show_cartoon",
"tags": [],
"reasons": {}
},
{
"tool": "show_sticks",
"tags": [],
"reasons": {}
},
{
"tool": "hide_atoms",
"tags": [],
"reasons": {}
},
{
"tool": "zoom_to",
"tags": [],
"reasons": {}
},
{
"tool": "set_background",
"tags": [],
"reasons": {}
},
{
"tool": "label_residues",
"tags": [],
"reasons": {}
},
{
"tool": "clear_labels",
"tags": [],
"reasons": {}
},
{
"tool": "reset_view",
"tags": [],
"reasons": {}
},
{
"tool": "take_snapshot",
"tags": [],
"reasons": {}
},
{
"tool": "start_recording",
"tags": [],
"reasons": {}
},
{
"tool": "stop_recording",
"tags": [],
"reasons": {}
},
{
"tool": "spin",
"tags": [],
"reasons": {}
},
{
"tool": "record_spin",
"tags": [],
"reasons": {}
},
{
"tool": "measure_distance",
"tags": [],
"reasons": {}
},
{
"tool": "measure_angle",
"tags": [],
"reasons": {}
},
{
"tool": "align_and_rmsd",
"tags": [],
"reasons": {}
},
{
"tool": "find_contacts",
"tags": [],
"reasons": {}
},
{
"tool": "get_bfactors",
"tags": [],
"reasons": {}
},
{
"tool": "measure_buried_area",
"tags": [],
"reasons": {}
},
{
"tool": "select_atoms",
"tags": [],
"reasons": {}
},
{
"tool": "select_near",
"tags": [],
"reasons": {}
},
{
"tool": "select_chain",
"tags": [],
"reasons": {}
},
{
"tool": "invert_selection",
"tags": [],
"reasons": {}
},
{
"tool": "name_selection",
"tags": [],
"reasons": {}
}
],
"surfaceDigest": "b8ad42cb4327b5ad876fb37f1b3cff3b53abe32ec20b1d9ec1f603eeef41180b",
"stats": {
"tools": 39,
"prompts": 0,
"resources": 0,
"findingsBySeverity": {
"critical": 0,
"high": 2,
"medium": 1,
"low": 1,
"info": 1
}
}
}