Skip to main content
Glama
Sign In
MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

util_ss

Idempotent

Colors molecular structures by secondary structure to visually distinguish helices, sheets, and loops; optionally limit recoloring to a selection.

Instructions

Colors by secondary structure

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "util_ss"
  }
}

Input Schema

NameRequiredDescriptionDefault
selectionNoWhat to recolour. Defaults to everything.all

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.5.1
    • addedInput schema / properties / selection / description
      Added value: +"What to recolour. Defaults to everything."
  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 idempotentHint=true, destructiveHint=false, and openWorldHint=false, so the safety profile is covered. The description adds nothing beyond that: it does not say which color scheme is applied, whether it overrides existing colors, or whether the original colors can be restored, which is the context an agent actually needs for a state-changing operation.

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 four-word fragment with no wasted wording and is front-loaded as a statement of purpose. Its brevity also amounts to under-specification, since no sentence supplies the context that is missing.

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. However, for a coloring utility competing with many color-related siblings, the definition omits essentials: which scheme is used, whether it acts on a specific object, and how it relates to util_color_secondary, leaving the agent to guess.

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?

There is a single optional parameter, and schema coverage is 100%: the schema already explains that 'selection' means what to recolor and defaults to everything. The description adds no meaning beyond that, 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 fragment 'Colors by secondary structure' does name a verb and a resource, so an agent knows it recolors something according to secondary structure. However, it never says what is recolored or where this occurs, and it does not separate itself from close siblings such as util_color_secondary, color, or spectrum, so the purpose is only marginally distinguishable.

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 prerequisite such as the need to have a structure loaded with secondary-structure annotations, and no mention of alternatives. The agent must infer from the sibling list alone whether to pick this tool or util_color_secondary.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Deploy Server

Other Tools