Skip to main content
Glama

load_structure

Load a molecular structure from a local file (PDB, MMCIF) and apply a BFS multimer heuristic to group chains based on a specified distance cutoff.

Instructions

Loads a structure from a local file path and applies the BFS multimer heuristic.

Args: file_path: Path to the structure file (PDB, MMCIF, etc.) obj_name: Name for the object in PyMOL multimer_cutoff: Distance (A) between chains to keep them in the same multimer. Default 8.0A is suitable for most functional assemblies.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
obj_nameYes
file_pathYes
multimer_cutoffNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations provided, so description must disclose behavior. It adds the multimer heuristic detail but lacks info on side effects, permissions, or output. Partially transparent.

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?

Very concise: 3 sentences plus arg list. Front-loaded with purpose, no unnecessary words.

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?

Output schema exists, so return explanation not needed. Covers all three parameters, though lacks error handling or supported formats. Adequate for a simple load 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?

Schema description coverage is 0%, so description must compensate. It explains file_path and obj_name briefly, and adds meaning to multimer_cutoff with default and suitability. Does not fully describe file format or naming conventions.

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?

Clearly states the action (loads) and resource (structure from local file path) and specifies a distinguishing heuristic (BFS multimer). Differentiates from fetch_structure which loads from remote.

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

Usage Guidelines4/5

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

Implies usage for local file loading with multimer grouping, and mentions default cutoff suitability. However, no explicit guidance on when not to use or alternatives beyond sibling names.

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