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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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sculpt_iterate

Destructive

Runs sculpting relaxation cycles on a PyMOL object or selected state, letting you refine geometry by specifying the number of iterations.

Instructions

Performs sculpting iterations

Input Schema

NameRequiredDescriptionDefault
objYesObject to relax.
stateNoState to relax. "-1" is the current state.-1
iterationsNoNumber of relaxation cycles to run, e.g. "10".10

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed8 schema fields changedv1.5.1
    • addedInput schema / properties / iterations / default
      Added value: +"10"
    • addedInput schema / properties / iterations / description
      Added value: +"Number of relaxation cycles to run, e.g. \"10\"."
    • removedInput schema / properties / obj / anyOf
      Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
    • removedInput schema / properties / obj / default
      Removed value: -"all"
    • addedInput schema / properties / obj / description
      Added value: +"Object to relax."
    • addedInput schema / properties / obj / type
      Added value: +"string"
    • addedInput schema / properties / state
      Added value: +{
+  "default": "-1",
+  "description": "State to relax. \"-1\" is the current state.",
+  "title": "State",
+  "type": "string"
+}
    • changedInput schema / required
      Previous value: -[
-  "iterations"
-]New value: +[
+  "obj"
+]
  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 flag this as destructive, non-read-only, and non-idempotent, so the safety profile is partly covered. The description adds nothing beyond that: it does not say that coordinates are modified in place, whether the change is reversible, or whether it depends on a prior sculpt_activate call — all critical for a destructive mutation.

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 filler, so it is not bloated. However, brevity here comes from under-specification rather than tightness — the one sentence carries no actionable information.

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?

An output schema exists, so return values need not be explained, but for a destructive three-parameter geometry mutation the description is far too thin. It omits what sculpting does, prerequisites (sculpt_activate/sculpt_deactivate), and the in-place modification semantics that an agent needs before invoking it.

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 obj, state ("-1" = current state), and iterations all documented in the schema itself. The description contributes no additional meaning about the parameters, so the baseline of 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?

"Performs sculpting iterations" is essentially a restatement of the tool name (sculpt_iterate) with no added specificity. It never says what sculpting/relaxation actually does to the object (e.g., energy-minimizes or relaxes atomic coordinates), nor how it differs from siblings like sculpt_activate, sculpt_deactivate, or alter_state.

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 that sculpting must typically be activated first (sculpt_activate), no indication of when to prefer this over rebuild/alter_state, and no exclusions. A user must infer the entire workflow from sibling names.

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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