Skip to main content
Glama

save_session

Preserve the full PyMOL visual state by saving a session to a .pse file, capturing all objects, selections, colors, and camera views for exact restoration.

Instructions

Saves the entire PyMOL session to a .pse file.

A session captures everything — every object, selection, representation, colour, scene and the camera — so the work can be reopened exactly as it was. Use this before experimenting with a scene you would not want to rebuild, and to hand a finished figure to a colleague.

Unlike save, which writes bare coordinates, this preserves the whole visual state.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
filenameYesPath to write. A ``.pse`` extension is added if missing.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

With no annotations, the description carries the transparency burden. It states that the session captures every object, selection, representation, color, scene, and camera, and preserves the full visual state. It doesn't mention whether an existing file is overwritten or what the return value is, but the core behavioral scope is clearly disclosed.

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?

Three tightly written sentences: the first states the action, the second explains why and when to use it, and the third contrasts with 'save.' Every sentence contributes value, and the key information is front-loaded.

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

Completeness5/5

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

For a single-parameter tool with a well-described schema and an output schema, the description is complete: it explains the full scope of the session capture, gives practical use cases, and explicitly distinguishes the tool from the related 'save' command. No important behavioral or usage details are missing.

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 covers the only parameter fully, including that a .pse extension is added if missing. The tool description reinforces that the output is a .pse file but adds no additional parameter-level meaning beyond the schema, so the baseline of 3 applies.

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?

The description opens with a specific verb and resource: 'Saves the entire PyMOL session to a .pse file.' It clearly differentiates from the sibling tool 'save' by noting that save writes bare coordinates while this preserves the whole visual state.

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

Usage Guidelines5/5

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

Explicit guidance is provided: use before experimenting with a scene you might not want to rebuild, and to hand a finished figure to a colleague. It also names 'save' as the alternative for bare coordinates, giving clear when-to-use versus when-not-to-use context.

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