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electrostatic_view

Colors a protein molecular surface by approximate electrostatic potential using a red-white-blue spectrum, highlighting charged regions with atom- or residue-based charge assignment.

Instructions

Colors the molecular surface by approximate residue-based electrostatics.

Surface is colored red→white→blue via a B-factor spectrum. A white cartoon is shown beneath a semi-transparent surface. Organic ligands shown as sticks with yellow carbons.

For a more accurate Poisson-Boltzmann electrostatic surface, use poisson_boltzmann_view (requires APBS and PDB2PQR to be installed).

Args: obj_name: PyMOL object name (e.g. "1abc") mode: Charge assignment strategy. "atomic" (default) — charges assigned only to terminal charged atoms (e.g. ARG NH1/NH2/NE, LYS NZ, ASP OD1/OD2, GLU OE1/OE2, HIS ND1/NE2). Produces localized color at charge centers with natural falloff to white. "residue" — charges assigned uniformly to all atoms in each charged residue. Produces saturated patches; useful for quickly locating charged regions.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
modeNoatomic
obj_nameYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior5/5

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

With no annotations provided, the description bears full responsibility for behavioral disclosure. It thoroughly explains the coloring method (red-white-blue via B-factor spectrum), the display elements (white cartoon, semi-transparent surface, organic ligands as sticks with yellow carbons), and the charge assignment strategies for each mode.

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 concise and well-structured, with a clear header sentence explaining the core purpose, a paragraph on visual output, and a structured Args section. No unnecessary words.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's complexity (2 parameters, output schema present), the description covers all essential aspects: purpose, visual appearance, mode options, and alternative tool. It is sufficiently complete for an agent to select and invoke the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The schema has no descriptions (0% coverage), so the description entirely compensates. It provides detailed semantics for both parameters: obj_name is a PyMOL object name, and mode explains two strategies (atomic and residue) with their effects.

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 clearly states the tool colors the molecular surface by approximate residue-based electrostatics, using a red-white-blue spectrum. It distinguishes itself from the sibling poisson_boltzmann_view by noting the latter is for more accurate Poisson-Boltzmann surfaces.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly tells when to use this tool (approximate electrostatics) and when to use an alternative (poisson_boltzmann_view for more accurate results). It also explains the two modes (atomic vs residue) and their appropriate usage.

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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