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pocket_view

Visualize the binding pocket around a ligand as a colored surface, revealing chemical character, sidechains, H-bonds, and protein context for structural analysis.

Instructions

Visualizes the binding pocket cavity around a ligand as a colored surface.

The pocket (all residues within 5 Å of the ligand) is shown as a semi-transparent surface colored by chemical character: orange=hydrophobic, white=polar, skyblue=positive, salmon=negative. Pocket residue sidechains are shown as sticks. The ligand is shown as yellow sticks. H-bonds between the ligand and pocket are drawn as cyan dashes. The protein backbone is shown as a thin grey cartoon for context.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
resnYesLigand residue name (e.g. "ATP", "LIG", "ANP")
obj_nameYesPyMOL object name (e.g. "1abc")

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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 thoroughly describes the visual output: pocket surface with color coding by chemical character, sidechain sticks, ligand sticks, H-bond dashes, and cartoon backbone. It also specifies the 5 Å definition, adding meaningful behavioral details beyond the bare name.

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 multi-sentence but each sentence contributes a specific visual element (surface, sidechains, ligand, H-bonds, cartoon). The purpose is front-loaded in the first sentence, and there is no redundant filler.

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 visualization tool, the description provides a complete picture of the rendered scene, including color schemes and structural representations. It could mention prerequisites (e.g., object loaded, ligand present) or whether it modifies the existing view, but an output schema exists to cover return values, so the description is sufficiently complete for selection and invocation.

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?

The input schema fully describes both parameters (resn and obj_name) with examples, and the description does not add parameter-specific details. Since schema coverage is 100%, the baseline of 3 is appropriate.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('Visualizes') and resource ('the binding pocket cavity around a ligand'), and distinguishes itself from sibling tools like ligand_view or hydrophobic_surface_view by specifying the pocket-focused surface with residue sidechains and H-bonds.

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 intended use case is strongly implied (visualizing a binding pocket around a ligand with a 5 Å cutoff), but there are no explicit when-to-use or when-not-to-use instructions, nor references to alternative tools for different visualization needs.

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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