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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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align

DestructiveIdempotent

Move one molecular selection onto another target selection in PyMOL, keeping the target fixed, to compare or superimpose structures.

Instructions

Aligns one selection to another

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": {
      "mobile": "<mobile>"
    },
    "name": "align"
  }
}

Input Schema

NameRequiredDescriptionDefault
mobileYesSelection to move.
targetNoSelection to align onto; this one stays put.all
optionsNoExtra arguments, e.g. ``cycles=0`` to disable outlier rejection.

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed3 schema fields changedv1.5.1
    • addedInput schema / properties / mobile / description
      Added value: +"Selection to move."
    • addedInput schema / properties / options / description
      Added value: +"Extra arguments, e.g. ``cycles=0`` to disable outlier rejection."
    • addedInput schema / properties / target / description
      Added value: +"Selection to align onto; this one stays put."
  2. First observedv1.2.1

TDQS

C2.7/5.0
Behavior2/5

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

Annotations already declare destructiveHint=true, readOnlyHint=false, and idempotentHint=true, so the agent knows this mutates state, but the description adds no behavioral context of its own. It does not say that the mobile selection's coordinates are permanently transformed, that outlier rejection is applied by default (only hinted at obliquely by the options example), or that a fit score is returned. For a state-changing structural tool this is thin.

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?

Five words contain no filler and are front-loaded, but the terseness is under-specification rather than efficiency. There is room to add a clause about what gets moved without bloating the definition.

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?

An output schema exists, so return values need not be explained, and all three parameters are documented in the schema, which covers most of what an agent needs to call it. What is missing is the routing information relative to the many alignment siblings and confirmation that the mobile object is transformed in place.

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%, so the parameter meanings ('Selection to move', 'Selection to align onto; this one stays put', options example with cycles=0) are already fully documented in the schema. The prose adds nothing beyond that, including the notable default target='all', so the baseline of 3 applies.

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 verb 'aligns' plus 'one selection to another' gives a minimal indication of the operation, but it never says what kind of alignment (structural superposition of atoms) or which objects are affected. Nothing in the text distinguishes it from siblings like super, rms_cur, or intra_fit, so an agent must infer the difference from names alone.

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 mention of when to prefer align over super, rms_cur, or superposition_view, and no prerequisites such as needing matching atom counts or pre-existing selections. The only usage clue comes from the schema parameter descriptions, not the prose.

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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