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clip

Adjust PyMOL's clipping planes to control molecule visibility by specifying which plane to move and distance in Angstroms.

Instructions

Adjusts the clipping planes

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
modeYesWhich plane to move: ``near``, ``far``, ``move`` (both), ``slab``, ``atoms``.
distanceNoHow far to move the plane, in Angstrom. Negative moves the other way.1

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations are provided, so the description carries the full burden. It only states 'Adjusts the clipping planes' without disclosing that this changes visibility/rendering, how distance interacts with modes, or any side effects. This is minimal but not misleading.

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

Conciseness5/5

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

The description is a single concise sentence, front-loaded with the action and target, with no unnecessary words.

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?

For a simple 2-parameter tool with full schema coverage and an output schema present, the description is minimally viable. However, it lacks usage context and is too terse to fully guide an agent in all situations.

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%, with mode and distance clearly explained in the input schema. The description itself adds no extra parameter semantics, so baseline 3 is appropriate.

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 uses a specific verb 'Adjusts' and a clear resource 'clipping planes,' making the tool's function evident. It is distinct from sibling tools like zoom or orient, which affect the view but not the clip planes directly.

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?

The description provides no guidance on when to use this tool versus alternatives such as viewport, zoom, or orient. There is no mention of exclusions, prerequisites, or specific scenarios.

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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