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.

Coordinates are read as RELION does: centred Angstrom coordinates (rlnCenteredCoordinateX/Y/ZAngst) relative to each tomogram's centre when it is known, from --tomograms-star or the tomograms already in the copick project; otherwise rlnCoordinateX/Y/Z in tilt-series pixels, the unit RELION 4 and 5 use (from --tilt-series-pixel-size, the file's optics table, or the tomograms.star); otherwise, for files written by other tools, in pixels of --voxel-size. --relion-version relion5 or relion4 forces centred or pixel coordinates. Subtomogram orientations (rlnTomoSubtomogram*) and shifts (rlnOrigin*Angst) are applied.

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	—	Voxel size in Angstrom. Selects the copick tomograms whose centres are used for centred coordinates, and is the unit of rlnCoordinateX/Y/Z when no tilt-series pixel size is known (then it is required).
`--tomograms-star`	file	—	Path to RELION tomograms.star giving each tomogram's centre and tilt-series pixel size. If not provided, centres are read from existing tomograms in the copick project.
`--tilt-series-pixel-size`	float	—	STAR only: tilt-series pixel size in Angstrom, the unit RELION 4/5 use for rlnCoordinateX/Y/Z. Read from the file's optics table (rlnTomoTiltSeriesPixelSize) when omitted.
`--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 particles whose coordinates are tomogram pixels at 10 A (no optics table)
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