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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

load_structure

DestructiveIdempotent

Load a structure from a local file into PyMOL and apply the BFS multimer heuristic to group chains by proximity, with options to replace the session or add to it.

Instructions

Loads a structure from a local file path and applies the BFS multimer heuristic.

Input Schema

NameRequiredDescriptionDefault
replaceNoClear the session first, so this is the only structure loaded. Pass False to add to what is already loaded — which is how you get two structures into one session for superposition_view.
obj_nameYesName for the object in PyMOL
file_pathYesPath to the structure file (PDB, MMCIF, etc.)
multimer_cutoffNoDistance (A) between chains to keep them in the same multimer. Default 8.0A is suitable for most functional assemblies.

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed4 schema fields changedv1.5.1
    • addedInput schema / properties / file_path / description
      Added value: +"Path to the structure file (PDB, MMCIF, etc.)"
    • addedInput schema / properties / multimer_cutoff / description
      Added value: +"Distance (A) between chains to keep them in the same multimer. Default 8.0A is suitable for most functional assemblies."
    • addedInput schema / properties / obj_name / description
      Added value: +"Name for the object in PyMOL"
    • addedInput schema / properties / replace
      Added value: +{
+  "default": true,
+  "description": "Clear the session first, so this is the only structure loaded. Pass False to add to what is already loaded — which is how you get two structures into one session for superposition_view.",
+  "title": "Replace",
+  "type": "boolean"
+}
  2. First observedv1.2.1

TDQS

A3.6/5.0
Behavior3/5

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

Annotations already declare destructiveHint=true and idempotentHint=true, so safety is covered. The description adds one genuinely non-obvious behavioral fact — that chains get grouped by a BFS multimer heuristic at load time — but never states that loading can clear the existing session or what happens on an unreadable path.

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?

One sentence, front-loaded with the action and the input source, with zero filler. Nothing redundant or padded.

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?

With annotations, a full output schema, and 100%-covered parameters, the description only needs to establish what the operation does and when to reach for it, which it largely does. The remaining gap is that "BFS multimer heuristic" is left as unexplained jargon the agent must either guess at or look up.

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 replace/multimer_cutoff entries are unusually explanatory, so the schema does the heavy lifting. The description's only link to parameters is the vague mention of the multimer heuristic, which never connects to multimer_cutoff or its default distance.

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?

States a specific verb+resource ("Loads a structure") scoped to "a local file path", which implicitly separates it from fetch_structure and load_session without naming them. The added clause about the BFS multimer heuristic further pins down what makes this load path distinctive, though no sibling is called out by name.

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

Usage Guidelines3/5

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

There is no explicit when-to-use or when-not-to-use guidance; the reader must infer that this is the entry point for local coordinate files rather than fetched or session data. The only routing hint lives in the schema's replace parameter (pointing to superposition_view), not in the description itself.

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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