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latent_traverse_view

Idempotent

Step through an ensemble's conformations as a contoured trajectory, holding contour level at a constant absolute value so density changes remain visible across frames.

Instructions

Step through an ensemble's conformations as a contoured trajectory.

Refuses when the generating method was never identified. That is SPEC invariant I2 working, not a failure: cryoDRGN's latent density can bear no relation to the truth while 3DVA's frames are linear interpolations no particle occupied, and rendering both the same way asserts something for one that holds only for the other.

The contour is held at a constant ABSOLUTE value and converted to each frame's own sigma. PyMOL normalises every map independently on load, so a fixed sigma level would contour each frame at its own scale and flatten away the density change the traversal exists to show.

No latent scatter and no density estimate are drawn, deliberately. In a 41-submission blind challenge most methods missed a genuinely present middle state, so an empty region of latent space is a region of unknown occupancy — never evidence that a conformation does not occur.

Input Schema

NameRequiredDescriptionDefault
nameNoPrefix for the isosurfaces (defaults to "<ensemble>_surf")
colorNoOne colour for every frame; a per-frame spectrum would encode frame index as if measuredskyblue
levelNoContour level. If omitted, 1.5 sigma against the first frame is used.
unitsNoUnits of `level`: "sigma" (read against frame 1) or "absolute"sigma
build_movieNoWire the frames to PyMOL's movie timeline so they can be stepped and played
ensemble_nameYesAn ensemble previously loaded through the load_ensemble tool

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.5.2

TDQS

A3.6/5.0
Behavior4/5

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

Annotations only declare readOnlyHint=false, idempotent, non-destructive; the description goes further by disclosing the refusal condition (invariant I2), why contours are held at a constant absolute level rescaled per frame, and that latent scatter/density estimates are deliberately omitted. This is real behavioral context the agent could not derive from the annotations, though the rationale is delivered discursively rather than as crisp operating rules.

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

Conciseness3/5

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

The purpose is correctly front-loaded in the first sentence, but the remaining two paragraphs are essayistic, spending substantial length on methodology philosophy ('41-submission blind challenge', 'latent density can bear no relation to the truth'). The insight is valuable but could be compressed to a fraction of the words.

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 moderately complex visualization tool with six parameters and an output schema, the description covers the key operational facts: it needs a method-identified ensemble, it builds a movie by default, and it renders only isosurfaces. Return-value explanation is correctly omitted since an output schema exists.

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 description coverage is 100%, so the baseline is 3. The description does add meaning to the level/units pairing by explaining that a fixed absolute value is converted into each frame's own sigma, but it says nothing about name, color, build_movie, or ensemble_name beyond what the schema already documents.

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 opening sentence gives a specific verb and resource: 'Step through an ensemble's conformations as a contoured trajectory.' It clearly distinguishes this from static views, but it never names a sibling such as density_view, ensemble_spread_view, or deformation_view, so the agent must infer the boundary from the ensemble/trajectory framing alone.

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 refusal clause ('refuses when the generating method was never identified') communicates a hard precondition, which is useful. However, there is no explicit when-to-use versus when-not guidance relative to the many neighboring view tools, and no statement of prerequisites like having called load_ensemble first beyond the schema.

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