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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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spheroid

Idempotent

Render atoms as smooth spheres for molecular structure visualization in PyMOL.

Instructions

Displays atoms as smooth spheres

Input Schema

NameRequiredDescriptionDefault
objNoObject to render as smoothed spheres. This is an object name, not a selection expression — cmd.spheroid resolves it as an object and reports 'Object not found' for anything else. The default is the empty string, which cmd.spheroid takes to mean every object; passing "all" is an error, because no object is named that.

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.5.2
    • changedInput schema / properties / obj / default
      Previous value: -"all"New value: +""
    • changedInput schema / properties / obj / description
      Previous value: -"Object to render as smoothed spheres. This is an object name, not a selection expression — cmd.spheroid resolves it as an object and reports 'Object not found' for anything else."New value: +"Object to render as smoothed spheres. This is an object name, not a selection expression — cmd.spheroid resolves it as an object and reports 'Object not found' for anything else. The default is the empty string, which cmd.spheroid takes to mean every object; passing \"all\" is an error, because no object is named that."
  2. Changed2 schema fields changedv1.5.1
    • addedInput schema / properties / obj
      Added value: +{
+  "default": "all",
+  "description": "Object to render as smoothed spheres. This is an object name, not a selection expression — cmd.spheroid resolves it as an object and reports 'Object not found' for anything else.",
+  "title": "Obj",
+  "type": "string"
+}
    • removedInput schema / properties / selection
      Removed value: -{
-  "anyOf": [
-    {
-      "type": "string"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": "all",
-  "title": "Selection"
-}
  3. 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, idempotentHint=true and destructiveHint=false, so the safety profile is covered structurally; the description adds nothing beyond them. It does not say whether an existing representation is replaced or added, or how the render state changes, which is exactly the context this mutation-flagged tool 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?

Five words contain no padding and are front-loaded, but the brevity is under-specification rather than efficiency. For a tool that changes visualization state, this is too thin to earn a high conciseness score.

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 the description still omits the essential behavioral facts: whether spheroid replaces or layers on other representations and how it relates to 'as'/'show'. Against ~80 siblings in a PyMOL control surface, that gap matters.

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% and the 'obj' parameter is documented thoroughly, including the empty-string-equals-all-objects and the 'all' error case. The description adds no parameter meaning whatsoever, 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 description gives a verb and a resource ('Displays atoms as smooth spheres'), so the basic effect is inferable, but it never distinguishes this from the generic representation setter sibling 'as' or from 'show'/'cartoon'/'isomesh', which all change how atoms are rendered. An agent cannot tell from the text why to pick spheroid over `as spheres`.

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 exclusions, and no mention of any alternative sibling. The only usage-relevant fact (that omitting the argument targets all objects) lives in the schema, not 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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