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MCPymol

MCPymol

by chemrich
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Python
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pharmacophore_view

Idempotent

Colors a ligand by pharmacophore feature type to visualize hydrogen-bond interactions, interacting residues, and the binding pocket in context.

Instructions

Colors a ligand by pharmacophore feature type.

The ligand is shown as sticks color-coded by pharmacophore property: violet=ring/aromatic carbon, yellow=aliphatic carbon, skyblue=nitrogen (H-bond donor/acceptor), salmon=oxygen (H-bond acceptor), gold=sulfur, palegreen=halogen (F/Cl/Br/I). H-bonds to protein are shown as cyan dashes. Interacting residue sidechains are shown as element-colored sticks with CA labels. The pocket is shown as a semi-transparent grey surface for cavity context. The protein backbone is shown as a thin grey cartoon.

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": {
      "obj_name": "<obj_name>",
      "resn": "<resn>"
    },
    "name": "pharmacophore_view"
  }
}

Input Schema

NameRequiredDescriptionDefault
resnYesLigand residue name (e.g. "ATP", "LIG", "ANP")
obj_nameYesPyMOL object name (e.g. "1abc")

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.5.1
    • addedInput schema / properties / obj_name / description
      Added value: +"PyMOL object name (e.g. \"1abc\")"
    • addedInput schema / properties / resn / description
      Added value: +"Ligand residue name (e.g. \"ATP\", \"LIG\", \"ANP\")"
  2. First observedv1.2.1

TDQS

A3.6/5.0
Behavior4/5

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

Annotations only tell the agent this mutates state (readOnlyHint=false) while being idempotent and non-destructive. The description goes well beyond that by specifying the exact resulting scene: ligand sticks recolored by feature, cyan H-bond dashes, labeled interacting sidechains, grey semi-transparent pocket surface, and a thin grey backbone cartoon. It does not say whether pre-existing representations are hidden or replaced, nor whether new objects are created, which is the main residual gap.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Purpose is front-loaded in the first sentence, and the color legend that follows is functional because it defines the output encoding the agent would otherwise have to guess. The residue/surface/cartoon sentences are shorter but still carry scene-information value; nothing is clearly padding.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present and full parameter documentation, the definition covers what the render looks like thoroughly. What it omits is operational context around a mutating visualization call: required prior state, whether the user's existing view is overwritten, and how it composes with other views.

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% with only two required parameters, and both are documented in-schema with examples ('ATP', '1abc'). The description adds nothing about them, which is acceptable but establishes the baseline 3 rather than anything higher.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

'Colors a ligand by pharmacophore feature type' gives a specific verb and resource, and the lettered color scheme makes the tool's scope unmistakable. It never names a sibling (e.g. ligand_view or hydrophobic_surface_view), so the agent has no explicit contrast, which keeps it at 4 rather than 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is only implied: an agent can infer this is for inspecting ligand–pocket pharmacophore complementarity. There is no statement of when to prefer it over ligand_view, pocket_view, or hydrophobic_surface_view, and no prerequisites such as needing the object loaded in PyMOL with the named residue present.

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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