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util_cbaw

Apply color-by-atom scheme with white carbons to molecular structures in PyMOL. Specify a selection to recolor, or default to all atoms.

Instructions

Colors by atom, white carbons (Color By Atom, White)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoWhat to recolour. Defaults to everything.all

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations exist, so the description carries the full burden. It only says 'Colors' without disclosing that it modifies existing colors, whether it applies to the selected atoms only or all objects, or any side effects. The behavior is implied but not transparent.

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 extremely concise and front-loaded with the key verb and target. It has no wasted words, though it could be slightly more structured or complete. It earns a 4 for efficiency.

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?

Given the simple nature (1 optional parameter) and the existence of an output schema, the description provides the minimum viable information. However, it lacks details about what 'by atom' means (e.g., element-based coloring), potential scope, or how it relates to siblings, leaving some gaps.

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?

Schema coverage is 100% for the single 'selection' parameter, so the schema already documents it. The description adds the general effect (white carbons) but no additional parameter-specific semantics beyond what the schema provides, which aligns with the baseline of 3.

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 states the action ('Colors') and the target ('atoms'), and specifies a distinguishing detail ('white carbons'). It clearly indicates this is a coloring utility, though the exact meaning of 'by atom' and how it differs from many sibling color tools is not fully explicit.

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?

No guidance is provided on when to use this tool versus the many alternative coloring utilities (e.g., util_cbc, util_cbag, util_rainbow). The description does not mention any context, prerequisites, or exclusions.

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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