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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

clip

Idempotent

Move near, far, slab, or atom cutoff planes by a specified Angstrom distance to control visible regions of a PyMOL structure.

Instructions

Adjusts the clipping planes

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "mode": "<mode>"
    },
    "name": "clip"
  }
}

Input Schema

NameRequiredDescriptionDefault
modeYesWhich plane to move: ``near``, ``far``, ``move`` (both), ``slab``, ``atoms``.
distanceNoHow far to move the plane, in Angstrom. Negative moves the other way.1

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.5.1
    • addedInput schema / properties / distance / description
      Added value: +"How far to move the plane, in Angstrom. Negative moves the other way."
    • addedInput schema / properties / mode / description
      Added value: +"Which plane to move: ``near``, ``far``, ``move`` (both), ``slab``, ``atoms``."
  2. First observedv1.2.1

TDQS

C2.5/5.0
Behavior2/5

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

Annotations already declare the safety profile (readOnlyHint=false, destructiveHint=false, idempotentHint=true), so the agent knows this mutates view state reversibly. The description adds nothing beyond that: it does not say whether the change is purely a viewer/camera state, whether it is reset by reset/zoom/orient, or whether it persists into saved sessions and renders.

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

Conciseness3/5

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

It is a single short sentence with zero waste, which is good, but it is under-specified rather than genuinely concise — the brevity comes from omitting information rather than from efficient phrasing. Nothing is front-loaded because there is essentially one clause.

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

Completeness2/5

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

Modes like 'slab' and 'atoms' are non-obvious and the visible effect of adjusting near/far planes is not described; an agent could invoke this without understanding the outcome. The presence of an output schema excuses not explaining return values, but the core behavioral explanation for a view-manipulating tool is largely absent.

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%, with mode enumerating near/far/move/slab/atoms and distance documented in Angstrom including negative direction. The description contributes no additional parameter meaning, so this sits at the baseline of 3 where the schema carries the semantics.

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

Purpose3/5

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

The description names a concrete resource ('clipping planes') and a soft verb ('adjusts'), so the domain is identifiable. However, it does not say what clipping planes are in this context or how this differs from camera/display siblings such as viewport, zoom, orient, or move, leaving the agent to infer the distinction.

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

Usage Guidelines2/5

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

There is no when-to-use guidance at all: no indication of when clipping adjustment is needed (e.g., cutting away foreground atoms to inspect an interior cavity), no prerequisites, and no mention of alternative tools. The agent must already know PyMOL semantics to decide to call this.

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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