poisson_boltzmann_view

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

Annotations only say this is a non-read-only, idempotent, non-destructive operation; the description adds the behavior that actually matters: it shells out to PDB2PQR and APBS, requires them to be installed, fixes AMBER force field and pH 7.0, and hardcodes a ±20 kT/e color scale. What it does not disclose is roughly how expensive/slow the external computation is or that PyMOL objects are created as a side effect.

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

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

Front-loaded with the outcome, then mechanism, then rendering details, then prerequisites — a sensible order with no filler prose. The install command block is slightly more verbose than an agent needs, but it is genuinely actionable information rather than padding.

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

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

For a one-parameter, externally-dependent visualization tool with an output schema, the description covers mechanism, dependencies, and visual result, which is enough to call it correctly. The remaining gap is not warning that missing APBS/PDB2PQR will cause failure rather than a fallback.

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

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

Schema coverage is 100% with a single parameter already documented as the PyMOL object name. The description adds nothing about obj_name — not what object type it should be, nor what happens if the object lacks a surface — so the baseline 3 applies.

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

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 by true Poisson-Boltzmann electrostatic potential') plus the method used (PDB2PQR + APBS). The word 'true' and the explicit method distinguish it from the neighboring approximate electrostatic_view, even though that sibling is not named.

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

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

Usage is implied by the physics described, but there is no explicit statement of when to choose this over electrostatic_view or hydrophobic_surface_view. The closest thing to guidance is the prerequisite block, which tells the agent the tool cannot run without external binaries but not when it should be preferred.

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