copick add ctf
core
Set the CTF fits of a tilt series from a file.
Usage
Description
Reads per-image defocus, astigmatism and phase shift from an AreTomo3 _CTF.txt, a CTFFIND4 output file, a Warp tilt-series XML or a RELION tomograms.star, and stores them on the matching sections of a writable tilt series.
Arguments
| Argument | Description |
|---|---|
PATH |
The CTF file. |
Options
| Option | Type | Default | Description |
|---|---|---|---|
-c, --config |
path | — | Path to the configuration file. |
--run |
text | required | The run. |
--ts-type |
text | raw |
The tilt series. |
--format |
choice (aretomo3 | ctffind4 | warp | relion) | — | Format of PATH. Default: from its name (_CTF.txt, .txt, .xml, .star). |
--tomo-name |
text | — | RELION: the tomogram. Default: the run name. |
--section-map |
choice (auto | index | sorted | angle) | auto |
How the rows of a file map to tilt-series sections: 'auto' (the file's default), 'index' (row i is section i), 'sorted' (rows in ascending angle pair with sections in ascending nominal angle) or 'angle' (nearest nominal angle). |
--angle-tolerance |
float | 1.0 |
Largest difference in degrees between a row's angle and the nominal angle of its section. |
--debug / --no-debug |
boolean flag | False |
Enable debug logging. |