High-risk tools in ChimeraX MCP Server
10 of the 39 tools in ChimeraX MCP Server are classified as high risk. This page profiles those tools specifically, with recommended policy actions and the attack patterns that target them.
Every operation listed below is an action PolicyLayer recommends controlling at the transport layer. Open any tool to see the full profile, risk score, and YAML policy snippet.
Tools at high risk
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align_and_rmsdExecuteAlign one selection to another and report RMSD.
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invert_selectionExecuteInvert the current selection.
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minimize_energyExecuteRun energy minimization on a model.
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mutate_residueExecutemutate_residue
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reset_viewExecuteReset to the default camera view.
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run_scriptExecuteRun a ChimeraX command script (.cxc) or Python script (.py).
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show_electrostatic_surfaceExecuteCalculate and display Coulombic electrostatic potential on the surface.
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show_hydrophobicity_surfaceExecuteCalculate and display Molecular Lipophilicity Potential on the surface.
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spinExecuteSpin/rotate the model around an axis (x, y, or z).
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start_recordingExecuteStart recording a movie of the ChimeraX session.
Attacks that target this class
High-risk tools in any server share these documented attack patterns. Each links to the full case and the defensive policy.