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altloc_view

Idempotent

Display all alternate-location groups in a PyMOL object at once, color-coded by group with occupancy labels, so multiconformer heterogeneity is visible instead of one default conformation.

Instructions

Show every altloc group at once, one colour per group, occupancies labelled.

A multiconformer model says "at this site, these discrete alternatives, in these proportions". PyMOL shows one of them by default, which quietly turns a statement about heterogeneity into a single structure.

Input Schema

NameRequiredDescriptionDefault
labelNoLabel each alternate location with its occupancy value (default True)
obj_nameYesPyMOL object name (e.g. "1ejg")

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.5.1

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already declare the safety profile (non-read-only, idempotent, non-destructive), so the description only needs to add context. It does imply the tool creates colours and labels in the scene, consistent with readOnlyHint=false, but never says what happens to pre-existing representations, whether the colouring/labels must be cleared afterwards, or how it behaves on an object with no alternate locations.

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 actionable content is front-loaded in the first sentence, with no wasted clauses. The second sentence is explanatory framing rather than instruction — useful for justifying the tool's existence, but it occupies half the description without telling the agent anything it must do.

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 two-parameter visualization helper with full schema coverage and an output schema, the description covers purpose and rationale adequately. The remaining gap is preconditions (object must contain altlocs) and cleanup of the scene state it mutates, which would matter for repeated calls.

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% and both parameters are documented in the schema, so the baseline applies. The phrase "occupancies labelled" loosely corresponds to the `label` flag but the description never says the labelling can be turned off or what `obj_name` expects beyond the schema's own example.

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 first sentence gives a specific verb and resource ("Show every altloc group") plus concrete visual behavior (one colour per group, occupancies labelled). It is clearly distinguishable from siblings such as occupancy_view or ensemble_spread_view in substance, but it never names or contrasts with them, so an agent must infer the boundary itself.

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?

Usage is only implied via the second sentence about multiconformer models and PyMOL's default single-conformer display. There is no explicit "use this when X, prefer Y otherwise" routing, no mention of the nearest alternatives (occupancy_view, ensemble_spread_view), and no stated prerequisite that the loaded object must actually contain altlocs.

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