Skip to main content
Glama

dihedral

Calculate and visualize dihedral angles between four atom selections in degrees, drawing a named object for backbone phi/psi and ligand torsion analysis.

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

TableJSON 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

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

With no annotations provided, the description carries the full burden. It discloses two behaviors: measuring the angle and drawing the measurement as a named object. However, it remains ambiguous whether the angle is returned as a value or only drawn, and it does not mention failure modes or prerequisites. Some behavioral context is provided, but gaps remain.

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

Conciseness5/5

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

The description is two sentences with no wasted words. It front-loads the core measurement function, then adds the side effect and use cases. This is appropriately sized and well structured.

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

Completeness4/5

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

Given the tool has 5 parameters all documented in the schema and an output schema exists, the description covers the essentials: purpose, unit (degrees), side effect (drawing), and example use cases. It does not explain return values (covered by output schema) or state dependence, but for a measurement tool it is substantially complete. A slight gap is the lack of mention about state or structure requirements, so a 4.

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 the schema itself provides detailed parameter descriptions, including examples like 'For a backbone phi angle this is the preceding C.' The description adds no additional semantic meaning beyond what the schema already supplies, so the baseline of 3 is appropriate.

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

Purpose5/5

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

The description clearly states the tool measures the dihedral (torsion) angle between four selections in degrees, which is a specific verb+resource. It distinguishes itself from sibling tools like angle (three selections) and distance by explicitly mentioning four selections and torsion angle. The added note about drawing a named dihedral object further clarifies its function.

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?

The description gives clear context on when to use the tool: 'Useful for backbone phi/psi angles and ligand torsions.' It does not explicitly state when not to use it or name alternatives, but the provided use cases effectively guide an agent toward appropriate scenarios. Lacks explicit exclusions, so a 4 rather than 5.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/chemrich/MCPymol'

If you have feedback or need assistance with the MCP directory API, please join our Discord server