Skip to main content
Glama

crosslink_view

Idempotent

Highlights disulfide bonds and metal-ion coordination in a PyMOL structure, showing labeled cysteine side chains, yellow bond dashes, and orange metal spheres for structural inspection.

Instructions

Highlights structural cross-links: disulfide bonds, metals, and their coordination.

Protein backbone shown as a thin grey cartoon. Cysteine side chains (CA→CB→SG) shown as yellow sticks, labeled by residue. Disulfide bonds drawn as yellow dashes. Metal ions shown as orange spheres. Metal coordination bonds drawn as dashed lines to nearby protein atoms. Black background.

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>"
    },
    "name": "crosslink_view"
  }
}

Input Schema

NameRequiredDescriptionDefault
obj_nameYesPyMOL object name (e.g. "1abc")

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.5.1
    • addedInput schema / properties / obj_name / description
      Added value: +"PyMOL object name (e.g. \"1abc\")"
  2. First observedv1.2.1

TDQS

B3.4/5.0
Behavior4/5

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

With readOnlyHint=false and idempotentHint=true already declared, the description's job is to say what the scene mutation looks like, and it does: thin grey backbone cartoon, yellow cysteine sticks labeled by residue, yellow disulfide dashes, orange metal spheres, dashed coordination lines, black background. What it omits is whether the operation clears or layers onto existing representations and whether the camera is reset — meaningful gaps for a scene-mutating preset.

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 lead sentence states the purpose up front, followed by a compact rendering specification. Each sentence maps to a distinct visual element with no filler, though the color/geometry inventory is dense enough that it reads more as a spec sheet than guidance.

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?

An output schema exists, so return values need no explanation, and the description thoroughly covers the resulting visual state. However, for a tool that mutates the scene (readOnlyHint=false), it never addresses preconditions or interaction with prior representations, which is the main thing an agent needs before invoking it.

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?

Only one parameter exists and its schema description is complete ('PyMOL object name (e.g. "1abc")'), so the baseline is 3. The description adds nothing about obj_name — it never says the object must be loaded or that the view applies to that object specifically — but the schema carries the load.

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?

The description names the specific resource (structural cross-links: disulfide bonds, metals, coordination) and what the tool produces (a highlighted view), which separates it from generic siblings like show, cartoon, or color. It never explicitly contrasts itself with other view presets such as ligand_view or interface_view, so it stops short of full sibling differentiation.

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 at all: no statement of what kind of structure warrants this view, no prerequisite that the object must already be loaded, and no alternative named if the target is a ligand or interface rather than a cross-link. The agent must infer the trigger condition purely from the phrase 'structural cross-links'.

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