Skip to main content
Glama

alter_state

Alter atomic coordinates of a molecular selection in a defined state using a mathematical expression.

Instructions

Alters atomic coordinates in a state

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
stateYes
selectionYes
expressionYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations, the description must disclose behavioral traits. It only says 'alters', which implies mutation, but does not specify if changes are reversible, require permissions, or affect other parts of the state. This is insufficient for safe invocation.

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

Conciseness2/5

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

The description is extremely concise (one short sentence) but lacks substance. It does not earn its place as it adds minimal value; more detail would improve usability.

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

Completeness1/5

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

Given three required string parameters and an output schema, the description is woefully incomplete. It fails to explain what 'selection' or 'expression' mean, how they relate to altering coordinates, or what the output contains.

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

Parameters1/5

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

The description provides no information about the three parameters (state, selection, expression). Schema description coverage is 0%, and the description does not compensate by explaining their purpose or expected formats.

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 states the tool alters atomic coordinates in a state, which is a clear verb and resource. However, it does not specify what kind of alterations are supported or how it differs from sibling tools like 'alter'.

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 on when to use this tool vs. alternatives. There is no mention of prerequisites, restrictions, or comparison to siblings such as 'alter' or 'move'.

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