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unbond

DestructiveIdempotent

Removes a bond between two specified atoms in PyMOL to correct molecular structures by clearing unwanted connections.

Instructions

Removes a bond between two atoms

Input Schema

NameRequiredDescriptionDefault
atom1YesFirst atom of the bond to remove.
atom2YesSecond atom of the bond to remove.

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.5.1
    • addedInput schema / properties / atom1 / description
      Added value: +"First atom of the bond to remove."
    • addedInput schema / properties / atom2 / description
      Added value: +"Second atom of the bond to remove."
  2. First observedv1.2.1

TDQS

B3.1/5.0
Behavior2/5

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

Annotations already declare destructiveHint=true, idempotentHint=true, and openWorldHint=false, so the safety profile is covered. The description adds nothing beyond that — it does not say what happens if no bond exists between the atoms, whether the change is session-only or persisted, or how it interacts with a structure's connectivity records.

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?

A single front-loaded sentence with zero filler. It is minimal, but nothing in it is redundant or padding.

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 two-parameter mutation on an annotated tool with an output schema, this is close to sufficient. What is missing is the atom-identifier convention and the failure mode when the bond does not exist, which matter for a destructive operation.

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 both parameters are documented as the first/second atom of the bond. The description adds no meaning beyond the schema, so the baseline of 3 applies; it notably does not clarify the expected atom identifier syntax.

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?

States a specific verb+resource ('Removes a bond') and the two operands, so the operation is unambiguous. It does not, however, differentiate itself from the sibling 'bond' tool (which presumably creates the inverse), which keeps it off a 5.

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?

No guidance on when to use this versus 'bond', 'delete', or 'remove', and no stated prerequisites such as the bond needing to already exist or atoms needing to be selected. The agent must infer all of that from the name alone.

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