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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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symexp

Generate crystallographic symmetry mates for a selected PyMOL object, creating prefixed copies within a set cutoff distance for structural analysis.

Instructions

Generates symmetry-related copies

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": {
      "prefix": "<prefix>",
      "obj_name": "<obj_name>",
      "selection": "<selection>"
    },
    "name": "symexp"
  }
}

Input Schema

NameRequiredDescriptionDefault
segiNoOptional segment identifier for the new objects.
cutoffNoDistance in Angstrom out to which to generate mates.20
prefixYesPrefix for the generated symmetry-mate objects.
obj_nameYesObject holding the crystal symmetry. Separate from the selection below: cmd.symexp needs both.
selectionYesSelection whose crystallographic neighbours to build.

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed8 schema fields changedv1.5.1
    • removedInput schema / properties / cutoff / anyOf
      Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
    • addedInput schema / properties / cutoff / description
      Added value: +"Distance in Angstrom out to which to generate mates."
    • addedInput schema / properties / cutoff / type
      Added value: +"string"
    • addedInput schema / properties / obj_name
      Added value: +{
+  "description": "Object holding the crystal symmetry. Separate from the selection below: cmd.symexp needs both.",
+  "title": "Obj Name",
+  "type": "string"
+}
    • addedInput schema / properties / prefix / description
      Added value: +"Prefix for the generated symmetry-mate objects."
    • addedInput schema / properties / segi / description
      Added value: +"Optional segment identifier for the new objects."
    • addedInput schema / properties / selection / description
      Added value: +"Selection whose crystallographic neighbours to build."
    • changedInput schema / required
      Previous value: -[
-  "prefix",
-  "selection"
-]New value: +[
+  "prefix",
+  "obj_name",
+  "selection"
+]
  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, idempotentHint=false and destructiveHint=false, so the safety profile is covered. The description adds nothing beyond that — it does not say that repeated calls create additional duplicate objects, how mates are named, what the cutoff default of 20 Å means in practice, or that the source object is left untouched.

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 short with no wasted clauses, but that brevity comes from under-specification rather than precision; the phrase "symmetry-related copies" is vague where a specific noun such as "crystallographic symmetry mates" would cost no extra length.

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?

For a 5-parameter object-creating tool with a sibling that also manipulates symmetry, one sentence is not enough. It omits what gets created, how it is named, and the relationship to set_symmetry; only the presence of an output schema mitigates the gap.

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%, including the subtle obj_name vs selection distinction, so the schema carries this dimension. The description adds no meaning beyond it, which lands at the baseline 3.

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?

"Generates symmetry-related copies" gives a verb and a loose resource, but "symmetry-related copies" is imprecise — it never says these are crystallographic symmetry mates of a selection built from a crystal-symmetry object, nor that new objects are created with a prefix. It does not distinguish itself from the sibling set_symmetry, which an agent could easily confuse it with.

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. that crystal symmetry must already be defined on an object), and no mention of alternatives such as set_symmetry or create. Usage is only inferable from the tool name.

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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