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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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alter_state

Destructive

Modify atomic coordinates within a specified molecular state using a selection and coordinate expression, such as x=x+10, to adjust structures in PyMOL.

Instructions

Alters atomic coordinates in a state

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": {
      "state": "<state>",
      "selection": "<selection>",
      "expression": "<expression>"
    },
    "name": "alter_state"
  }
}

Input Schema

NameRequiredDescriptionDefault
stateYesState to modify.
selectionYesAtoms to modify.
expressionYesAssignment over coordinates, e.g. ``x=x+10``.

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed3 schema fields changedv1.5.1
    • addedInput schema / properties / expression / description
      Added value: +"Assignment over coordinates, e.g. ``x=x+10``."
    • addedInput schema / properties / selection / description
      Added value: +"Atoms to modify."
    • addedInput schema / properties / state / description
      Added value: +"State to modify."
  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 readOnlyHint=false, destructiveHint=true and idempotentHint=false, so the safety profile is known. The description adds nothing beyond that: it does not say coordinates are permanently overwritten, whether the change is undoable, or how state/selection scope the edit, which is the exact information a destructive mutation needs.

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?

A single short sentence with no filler, but the brevity crosses into under-specification: nothing is front-loaded beyond the bare action, and not one sentence earns extra value for the caller.

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?

Output schema exists, so return values need no explanation, but for a destructive coordinate-mutating tool the description omits irreversibility, permission/state requirements, and how the selection bounds the edit. That leaves key risks undocumented.

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 coverage is 100%, and the schema itself documents all three parameters including the expression example 'x=x+10', so the baseline is 3. The description contributes no additional meaning about selection syntax, expression grammar, or what 'state' refers to.

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 does add the object of the mutation (atomic coordinates in a state), but it is essentially a restatement of the name alter_state and gives no way to distinguish it from siblings such as alter, set, sculpt_iterate, or execute_pymol_command, which can also change coordinates.

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 prerequisites (e.g. an object must be loaded), and no mention of which sibling to prefer for related coordinate edits. An agent must infer the use case entirely from the name and the schema.

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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