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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

fab

Builds a peptide chain from a one-letter amino acid sequence in PyMOL, with optional secondary-structure settings such as helix.

Instructions

Creates a peptide chain from a sequence

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": {
      "sequence": "<sequence>"
    },
    "name": "fab"
  }
}

Input Schema

NameRequiredDescriptionDefault
optionsNoExtra arguments, e.g. ``ss=1`` to build it as a helix.
sequenceYesOne-letter amino acid sequence, e.g. "ACDEFGH".

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.5.1
    • addedInput schema / properties / options / description
      Added value: +"Extra arguments, e.g. ``ss=1`` to build it as a helix."
    • addedInput schema / properties / sequence / description
      Added value: +"One-letter amino acid sequence, e.g. \"ACDEFGH\"."
  2. First observedv1.2.1

TDQS

C2.9/5.0
Behavior2/5

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

Annotations already declare it is a non-idempotent write (readOnlyHint=false, idempotentHint=false, destructiveHint=false), yet the description adds no behavior beyond that: it does not say whether an object is created and how it is named, whether existing objects are overwritten, or what effect repeated calls have.

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?

One short, front-loaded sentence with zero filler. It is efficient, though the terseness contributes to the missing behavioral detail rather than compensating for it.

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

Completeness3/5

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

An output schema exists and the parameters are fully documented, so the minimum is met for a simple two-parameter tool. However, for a PyMOL object-creating command, the description omits the one thing an agent most needs to know: what object gets created and how it is named.

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 'sequence' and 'options' both documented (including the ss=1 helix example), so the schema carries the parameter burden. The description adds no meaning beyond it, which is the baseline-3 case.

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 gives a concrete verb and resource ('Creates a peptide chain from a sequence'), which decodes the otherwise opaque name 'fab'. It does not distinguish the tool from near-neighbors such as 'fragment' or 'create', so an agent must infer the boundary, keeping it just short of a 5.

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, no mention of alternatives like 'fragment' or 'create', and no prerequisites. The agent learns what the tool does but nothing about when it is the right choice among ~130 siblings.

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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