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load_trajectory

Load GROMACS/DCD trajectories into PyMOL: read the structure file, then append frames as states. Ensure atom count and order match to avoid errors.

Instructions

Load a GROMACS/DCD trajectory: load the structure, then append frames as states.

Requires matching atom count/order (trjconv strip/reorder is the common pitfall).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
stopNoLast frame to load (-1 = all).
startNoFirst frame (1-based) to load.
intervalNoLoad every Nth frame (subsample to bound RAM).
object_nameNoObject name to create.traj
structure_pathYesTopology/first-frame file (.gro/.pdb) matching the trajectory atoms.
trajectory_pathYesTrajectory file (.xtc/.trr/.dcd) with the SAME atom set/order.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

No annotations are present, so the description carries the burden. It discloses that loading appends frames as states (a session mutation) and warns about the common trjconv pitfall. However, it does not address overwrite behavior or potential side effects on existing objects.

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?

Two sentences, no redundant filler, main purpose front-loaded. The warning is valuable and concise.

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?

The description covers the core workflow and a key pitfall, but omits usage guidance relative to load_trajectory_mda and gives no information about object overwrite semantics. Output schema covers returns, so that is not an issue.

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%, so the baseline is 3. The description adds context about atom matching relevant to structure_path and trajectory_path, but does not elaborate on start/stop/interval beyond the schema.

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 clearly states the action ('Load a GROMACS/DCD trajectory'), specifies the resource type, and outlines the process ('load the structure, then append frames as states'). It differentiates from the sibling load_trajectory_mda by explicitly naming GROMACS/DCD formats.

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

Usage Guidelines3/5

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

The description implies use for GROMACS/DCD trajectory files but does not explicitly contrast with load_trajectory_mda or provide when-not guidance. The atom-count warning is a prerequisite, not a usage rule.

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

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