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electrostatic_view

Idempotent

Color molecular surfaces by approximate residue-based electrostatics, highlighting charged regions with a red-white-blue spectrum for quick structural analysis.

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).

Input Schema

NameRequiredDescriptionDefault
modeNoCharge 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.atomic
obj_nameYesPyMOL object name (e.g. "1abc")

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.5.1
    • addedInput schema / properties / mode / description
      Added value: +"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."
    • addedInput schema / properties / obj_name / description
      Added value: +"PyMOL object name (e.g. \"1abc\")"
  2. First observedv1.2.1

TDQS

A4.3/5.0
Behavior4/5

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

With readOnlyHint=false but destructiveHint=false, the annotations already signal a state-changing but safe operation. The description adds substantial context the annotations cannot: the red→white→blue B-factor spectrum, the semi-transparent surface over a white cartoon, and yellow-carbon ligand sticks. It stops short of saying what existing representations are replaced or how to restore prior coloring (restore_bfactors exists as a sibling), which is the one behavioral gap.

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?

Front-loaded with the core action and then the visual result, with the alternative deferred to a clearly separated sentence. The color and ligand details are slightly decorative but genuinely help an agent predict the rendered output.

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?

Two parameters, 100% schema coverage, an output schema, and annotations covering the safety profile — the description fills the remaining gap by describing the visual result and the more-accurate alternative. Only the effect on pre-existing representations is unaddressed.

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% and the mode parameter's enum-like semantics (atomic vs residue) are fully documented in the schema, including examples of charged atoms. The description adds no syntax, default, or format detail for obj_name or mode, so this is the baseline 3.

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?

States a specific verb and resource (colors the molecular surface) with a clear qualifier (approximate residue-based electrostatics), which unambiguously separates it from rendering siblings like hydrophobic_surface_view or bfactor_view.

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?

Explicitly names the sibling poisson_boltzmann_view and the condition that selects it (more accurate PB surface, requires APBS and PDB2PQR). The agent knows both when this tool is the right choice and when to route elsewhere.

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