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MCPymol

MCPymol

by chemrich
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Python
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dihedral

Idempotent

Measures the torsion angle between four atom selections in degrees and draws a named measurement object for backbone phi/psi or ligand torsions.

Instructions

Measures the dihedral (torsion) angle between four selections, in degrees.

Also draws the measurement as a named dihedral object. Useful for backbone phi/psi angles and ligand torsions.

Input Schema

NameRequiredDescriptionDefault
nameNoName for the dihedral object.
selection1NoFirst atom of the torsion. For a backbone phi angle this is the preceding C.(pk1)
selection2NoSecond atom; the first of the two forming the rotatable bond.(pk2)
selection3NoThird atom; the second of the two forming the rotatable bond.(pk3)
selection4NoFourth atom, at the far end of the torsion.(pk4)

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed5 schema fields changedv1.5.1
    • addedInput schema / properties / name / description
      Added value: +"Name for the dihedral object."
    • addedInput schema / properties / selection1 / description
      Added value: +"First atom of the torsion. For a backbone phi angle this is the preceding C."
    • addedInput schema / properties / selection2 / description
      Added value: +"Second atom; the first of the two forming the rotatable bond."
    • addedInput schema / properties / selection3 / description
      Added value: +"Third atom; the second of the two forming the rotatable bond."
    • addedInput schema / properties / selection4 / description
      Added value: +"Fourth atom, at the far end of the torsion."
  2. First observedv1.2.1

TDQS

A3.8/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The description discloses the key behavior beyond the name: the call also creates a persistent named dihedral object, which explains why readOnlyHint=false despite this being a measurement. It does not cover naming collisions, whether an existing object of the same name is overwritten, or how the selections are resolved, so significant behavioral questions remain open.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two short sentences: the operation and unit are front-loaded, followed by the practical use cases. There is no filler, though the second sentence blends a side effect and usage guidance in a way that slightly muddies the structure.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists and the input schema fully documents all five parameters, so the description needs only to convey purpose, side effect, and typical use, all of which it does. Nothing an agent needs in order to call it correctly appears to be missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100% and each selection's role in the torsion is already documented in the schema, including the phi-angle hint for selection1. The prose adds no parameter meaning beyond that, so the baseline of 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb and resource ("Measures the dihedral (torsion) angle between four selections") plus the unit (degrees) and a side effect (drawing a named dihedral object). It is clear and precise, though it never distinguishes itself explicitly from the sibling three-atom `angle` or `distance` tools.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

"Useful for backbone phi/psi angles and ligand torsions" gives concrete usage contexts that tell an agent which scientific situation calls for this tool. It stops short of explicit when-not guidance or naming an alternative tool to use instead.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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