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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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h_fill

DestructiveIdempotent

Fills open valences on the currently picked PyMOL atom with hydrogens, adding missing hydrogens to the GUI-picked atom without requiring a selection.

Instructions

Fills open valences on the currently picked atom with hydrogens.

Takes no selection: cmd.h_fill operates on PyMOL's editor pick, so it needs an atom picked in the GUI and cannot be aimed from here. Passing it a selection used to land the string in its quiet argument and fail with an integer conversion error. For adding hydrogens to a selection over the bridge, use h_add.

Input Schema

NameRequiredDescriptionDefault

No arguments

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.5.1
    • removedInput schema / properties / selection
      Removed value: -{
-  "anyOf": [
-    {
-      "type": "string"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": "all",
-  "title": "Selection"
-}
  2. First observedv1.2.1

TDQS

A4.7/5.0
Behavior4/5

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

The annotations already declare destructiveHint=true, idempotentHint=true and readOnlyHint=false, so the safety profile is covered. The description adds genuinely non-obvious behavior: the operation keys off PyMOL's editor pick rather than an argument, and a legacy argument-passing path fails with an integer conversion error. What it does not state is how many hydrogens get added or whether existing hydrogens are retained.

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?

The core action and its GUI precondition are front-loaded, then the alternative is routed. The historical note about the migrated `quiet` argument is slightly more detail than an agent strictly needs, but it is short and directly actionable.

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

Completeness5/5

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 described, and the annotations carry the mutation/idempotency profile. Combined with the pick requirement, the failure mode, and the h_add alternative, nothing an agent needs to call this correctly is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With zero parameters the baseline is 4, and this description earns the extra point by explaining why there is no selection argument and what happens if an agent tries to pass one. That preempts the single most likely parameter mistake for this tool.

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

Purpose5/5

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

The opening sentence names a specific verb and resource ('Fills open valences ... with hydrogens') plus the exact scope ('currently picked atom'). It also explicitly separates itself from the sibling h_add, so an agent can choose without opening either schema.

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

Usage Guidelines5/5

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

It states the precondition (an atom must be picked in the GUI), states what the tool cannot do from here, and names the correct alternative ('For adding hydrogens to a selection over the bridge, use `h_add`'). Both the when and the when-not are explicit.

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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