copick add picks-relion

core

Add picks from RELION STAR files containing multiple tomograms.

Usage

copick add picks-relion [OPTIONS] PATH

Description

Imports particle picks from one or more RELION particle STAR files that carry the _rlnTomoName column identifying each particle's tomogram; run names are extracted from that column automatically. Both RELION 4.x (pixel coordinates in rlnCoordinateX/Y/Z) and RELION 5.0 (centered Angstrom coordinates in rlnCenteredCoordinateX/Y/ZAngst) formats are supported, with the version auto-detected from the column names unless overridden by --relion-version.

For RELION 5.0, tomogram dimensions are needed to convert centered coordinates to absolute coordinates. Supply them with --tomograms-star, or omit it to read the dimensions from tomograms already present in the copick project.

Arguments

Argument	Description
`PATH`	Path to the RELION particles STAR file (.star) or a glob pattern.

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--object-name`	text	required	Name of the pickable object (must exist in config).
`--session-id`	text	`1`	Session ID for the annotation.
`--user-id`	text	`copick`	User ID for the annotation.
`--voxel-size`	float	required	Voxel size in Angstrom (required for coordinate conversion).
`--tomograms-star`	file	—	Path to RELION tomograms.star file for RELION 5.0 coordinate conversion. If not provided and RELION 5.0 format is detected, tomogram dimensions will be read from existing tomograms in the copick project.
`--relion-version`	choice (auto \| relion4 \| relion5)	`auto`	RELION version for coordinate format. 'auto' detects from column names.
`--max-workers`	integer	`4`	Maximum number of worker threads.
`--overwrite / --no-overwrite`	boolean flag	`False`	Overwrite the object if it exists.
`--create / --no-create`	boolean flag	`True`	Create the object if it does not exist.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Examples

# Import RELION 4.x particles
copick add picks-relion particles.star -c config.json --object-name ribosome \
    --voxel-size 10.0

# Import RELION 5.0 particles using a tomograms.star for dimensions
copick add picks-relion particles.star -c config.json --object-name ribosome \
    --voxel-size 5.0 --tomograms-star tomograms.star

# Import RELION 5.0 particles using existing copick tomogram dimensions
copick add picks-relion particles.star -c config.json --object-name ribosome \
    --voxel-size 5.0