Skip to main content
Glama

alter

Modify atomic properties in a given selection using expressions such as b=0 or chain='B'. Assign new values to atom attributes for targeted edits.

Instructions

Alters atomic properties in a selection

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionYesAtoms to modify.
expressionYesAssignment over atom properties, e.g. ``b=0``, ``chain='B'``, ``resi=str(int(resi)+100)``.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It merely states that atomic properties are altered but does not explain how the assignment expression is evaluated, whether the operation is reversible, or any side effects on the selection or molecular state. This is insufficient for a mutating tool.

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 a single, focused sentence with no filler or redundancy. It is appropriately sized for the tool's simplicity, conveying the essence without unnecessary words, which earns a high score for conciseness and structure.

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

Completeness2/5

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

Although the schema documents both parameters, the description lacks essential context about the expression language, selection behavior, and relationship to sibling tools. An agent would not know when to choose 'alter' over 'alter_state' or 'set', nor understand the impact of the assignment, leaving the description incomplete for a mutating tool.

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 schema already describes both parameters with clear titles and examples (e.g., ``b=0``, ``chain='B'``), achieving 100% coverage. The description adds no param-specific meaning beyond what the schema provides, so it meets the baseline for high schema coverage.

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?

The description uses the specific verb 'Alters' and identifies the resource as 'atomic properties in a selection,' clearly conveying the tool's core function. It distinguishes from siblings like 'alter_state' (which likely modifies state-level properties) by indicating the target scope, though it does not explicitly name alternatives.

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 is provided about when to use this tool versus alternatives such as 'set' or 'alter_state'. The description only states what the tool does without offering context, exclusions, or preferred scenarios, leaving the agent to infer usage.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/chemrich/MCPymol'

If you have feedback or need assistance with the MCP directory API, please join our Discord server