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save_session

DestructiveIdempotent

Save the complete PyMOL session to a .pse file, preserving objects, selections, scenes, colors, and camera state so you can reopen the exact visual setup later.

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

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

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.5.1

TDQS

A4.3/5.0
Behavior4/5

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

Annotations declare destructiveHint=true, but the description never warns that saving to an existing filename overwrites it — the one behavior an agent most needs to know for a destructive write. It does add real value beyond the annotations by enumerating what the session captures (objects, selections, representations, colours, scenes, camera).

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

Conciseness4/5

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

Front-loaded with the core action, then scope, then usage, then sibling contrast — a clean information order. The middle enumeration of session contents is slightly elaborate for a one-parameter tool but still earns its place by justifying why the whole visual state is preserved.

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 and the single parameter is fully described, so return values and argument semantics need not be covered. The remaining gap is the destructive overwrite behavior, which matters given destructiveHint=true and is not addressed anywhere in the description.

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 coverage is 100% and already documents the filename parameter including the automatic `.pse` extension rule. The description adds no syntax, path, or format detail beyond what the schema provides, so the baseline 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?

States a specific verb and resource ('Saves the entire PyMOL session to a .pse file') and explicitly contrasts with the sibling `save`, which writes bare coordinates. An agent can distinguish the two without opening either schema.

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?

Gives two concrete use cases ('before experimenting with a scene you would not want to rebuild', 'hand a finished figure to a colleague') and names the alternative tool with the condition that selects it. Nothing is left to inference about when to pick this over `save`.

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