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putty_view

Visualize protein flexibility by mapping crystallographic B-factors to cartoon tube thickness and color, with a transparent surface and ligand sticks.

Instructions

Visualizes protein flexibility using a putty (tube-width) representation.

The cartoon tube radius scales linearly with crystallographic B-factor: thin/blue = rigid/ordered regions, thick/red = flexible/disordered regions. A 70%-transparent surface is shown, also colored by B-factor. Organic ligands are shown as sticks with yellow carbons. Black background.

Input Schema

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

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

With no annotations provided, the description carries the full burden. It discloses the visual output details (tube radius, B-factor coloring, 70% transparent surface, ligand representation, black background) but does not mention side effects like scene modification, prerequisites such as a loaded object, or reversibility.

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

Conciseness5/5

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

The description is four sentences, each providing distinct visual detail without redundancy. The main purpose is front-loaded in the first sentence, and every sentence earns its place.

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

Completeness4/5

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

For a simple one-parameter view tool, the description thoroughly covers the visual output, and an output schema exists for return values. The only minor gap is the lack of explicit guidance on prerequisites (e.g., object must be loaded) or side effects on the scene.

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?

The input schema already provides full documentation for the single parameter obj_name, including a descriptive string and an example. The description adds no additional parameter semantics beyond what the schema specifies, which is acceptable given the 100% schema coverage.

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 description opens with 'Visualizes protein flexibility using a putty (tube-width) representation', clearly stating the verb and resource. It further specifies the B-factor scaling, colors, surface, and ligand representation, distinguishing it from sibling tools like bfactor_view or plddt_view.

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?

The description implies its use for protein flexibility visualization, but it does not explicitly state when to use it instead of alternatives like bfactor_view or plddt_view. No when-not scenarios or alternative tool references are provided.

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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