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bfactor_view

Color protein structures by crystallographic B-factor to distinguish rigid (blue) from flexible (red) regions, highlighting dynamic loops and disordered termini.

Instructions

Colors the structure by crystallographic B-factor (temperature factor).

Blue = rigid/ordered (low B), white = intermediate, red = flexible/disordered (high B). Useful for identifying dynamic loops, disordered termini, and rigid structural cores. Shown as cartoon on black background.

Args: obj_name: PyMOL object name (e.g. "1abc")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
obj_nameYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

With no annotations provided, the description carries the full burden. It details the color mapping (blue-white-red), representation (cartoon), and background (black), providing transparency about the visual output. It does not describe side effects or persistence, but the behavioral information is adequate.

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 description is concise, with two main sentences and an Args line. It front-loads the purpose and adds detail efficiently. Slightly more structure could help, but overall it's well-sized.

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?

Given that an output schema exists (though not shown), the description does not need to explain return values. It covers what the tool does, how it works, and the parameter. It could mention if it modifies the object or just the view, but it's still complete for a coloring tool.

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

Parameters4/5

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

While schema coverage is 0%, the description includes an 'Args' section that explains the obj_name parameter, adding meaningful context beyond the schema (which only says 'string'). The example also clarifies usage.

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 clearly states the tool colors a structure by B-factor, a specific verb+resource. It distinguishes from sibling tools like 'color' or 'spectrum' by specifying the property used (B-factor) and the color scheme (blue-white-red).

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

Usage Guidelines4/5

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

The description explains when the tool is useful (identifying dynamic loops, disordered termini, rigid cores), but does not explicitly mention when not to use it or suggest alternatives. However, the context is clear and helpful.

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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