Recolors selected atoms by atom type, assigning yellow to carbons, to distinguish carbon atoms in a PyMOL structure. Use the selection option to target all or part of the model.
Colors by atom, yellow carbons (Color By Atom, Yellow)
| Name | Required | Description | Default |
|---|---|---|---|
| selection | No | What to recolour. Defaults to everything. | all |
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |
Changes observed during successful MCP inspections.
v1.5.1Input schema / properties / selection / descriptionAdded value: +"What to recolour. Defaults to everything."v1.2.1Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The annotations already state that this operation is non-read-only, idempotent, and non-destructive, while the description adds the concrete effect of turning carbons yellow when coloring by atom. It does not explain persistence or scene-state implications, but that is a modest gap for a low-risk coloring utility.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is short and front-loads the action, but the parenthetical '(Color By Atom, Yellow)' largely repeats the name and does not add much information. It is still efficiently sized and avoids unnecessary bulk.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a one-parameter utility with an output schema and annotations, the definition covers the core effect and the parameter is documented in the schema. It remains incomplete for selecting among many similar color-by-atom variants because it offers no sibling differentiation or usage context.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, and the single 'selection' parameter is fully documented in the schema as what to recolor with a default of 'all'. The description adds no additional parameter semantics, so the baseline score of 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description names a specific action and color outcome: it colors atoms by atom type with yellow carbons. That is clear enough for the basic purpose, but it does not distinguish this variant from the many sibling util_cba* color-by-atom tools.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
There is no explicit when-to-use, when-not-to-use, or alternative-tool guidance. With numerous sibling color-by-atom commands available, an agent gets no help choosing this one over util_cbam, util_cbas, or the other variants.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.