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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

save

DestructiveIdempotent

Exports molecular structures or full PyMOL sessions to chosen file formats for storage, analysis, or sharing.

Instructions

Saves data to a file

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": {
      "filename": "<filename>"
    },
    "name": "save"
  }
}

Input Schema

NameRequiredDescriptionDefault
stateNoWhich state to save. "-1" is the current state, "0" writes all states.-1
filenameYesOutput path. The extension picks the format: ``.pdb``, ``.cif``, ``.sdf``, ``.mol2``, ``.obj``, or ``.pse`` for a full session.
selectionNoWhat to write out.all

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed3 schema fields changedv1.5.1
    • addedInput schema / properties / filename / description
      Added value: +"Output path. The extension picks the format: ``.pdb``, ``.cif``, ``.sdf``, ``.mol2``, ``.obj``, or ``.pse`` for a full session."
    • addedInput schema / properties / selection / description
      Added value: +"What to write out."
    • addedInput schema / properties / state / description
      Added value: +"Which state to save. \"-1\" is the current state, \"0\" writes all states."
  2. First observedv1.2.1

TDQS

C2.3/5.0
Behavior2/5

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

Annotations already declare readOnlyHint=false, destructiveHint=true and idempotentHint=true, so the safety profile is covered structurally. The description adds nothing on top: it never warns that an existing file may be overwritten, that the format is chosen by extension, or what a "full session" (.pse) write implies.

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 no padding, but that brevity comes from under-specification rather than from disciplined editing. Nothing is front-loaded that helps an agent act.

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?

For a destructive write tool with three parameters and a sibling save_session, the description is too thin: it omits overwrite behavior, format selection rationale, and scope of what gets written. The presence of an output schema excuses return-value detail but not the mutation semantics.

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 each of state, filename and selection fully documented in the schema, including the extension-to-format mapping and the -1/0 state semantics. The description adds no parameter meaning beyond that, so the baseline 3 applies.

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

Purpose2/5

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

"Saves data to a file" restates the tool name with the vague object "data." It never says the data is molecular structure/session content, nor how it differs from the sibling save_session or print_export, so an agent cannot distinguish the write targets without reading the schema.

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 guidance on when to use this versus save_session, print_export, or png. The only implicit cue is the extension-based format list, which lives in the parameter schema rather than the description.

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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