copick new link
core
Link a tomogram to the alignment it was reconstructed with.
Usage
Description
Records which alignment (and thereby which tilt series) a tomogram was reconstructed with, so that
tomogram.alignment and tomogram.tilt_series find them. A writable tomogram records the link itself; a
read-only tomogram (e.g. of a static project or the CryoET Data Portal) is named by the alignment instead.
Options
| Option | Type | Default | Description |
|---|---|---|---|
-c, --config |
path | — | Path to the configuration file. |
--run |
text | required | Name of the run. |
--tomogram-uri |
COPICK_URI | required | The tomogram, as tomo_type@voxel_spacing. |
--alignment |
text | — | Name of the alignment of the run the tomogram was reconstructed with. |
--unlink |
boolean flag | False |
Remove the tomogram's link instead. |
--strict / --no-strict |
boolean flag | False |
Refuse a tomogram whose extent differs from the alignment's reference volume by more than a voxel. |
--debug / --no-debug |
boolean flag | False |
Enable debug logging. |
Examples
# Link a tomogram to an alignment
copick new link -c config.json --run TS_001 --tomogram-uri wbp@10.0 --alignment aretomo3
# Remove the link
copick new link -c config.json --run TS_001 --tomogram-uri wbp@10.0 --unlink
See also
copick rm alignment— remove alignments (and their links)