usage: This program extract particles from .ali files from IMOD reconstruction. It takes most information, including XTILT angle and boundary of trimmed volume from IMOD setting and log files. So make sure the whole IMOD project is not corrupted after the reconstruction. This program is test on IMOD 4.7.13 (10/15/2014). There is no garantee that it will work on project generated by any other IMOD versions. Extracting particles using the box locations saved in the info file corresponding to the tomogram [prog] --tomo <tomogram name> --edf <imod edf file> --ptclout <output 2D particle file name> [options] Extracting particles using 3D particles extracted from the tomogram [prog] --ptclin <3D particles> --edf <imod edf file> --ptclout <output 2D particle file name> [options]
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --tomo | str | File name of reconstructed tomogram. |
| --ptclin | str | File name of input 3D particles. |
| --edf | str | IMOD .edf file name. |
| --ptclout | str | File name of output 2D extracted particles. |
| --unbin | float | Unbin factor from input particles/tomogram to raw tilt. If unspecified, the program will calculate from the Apix of the header. |
| --boxsz | int | Box size of extracted 2D particles. |
| --defcol | int | Which column of ctf file is the defocus |
| --weight | None | Weight the particles by the variance of defocus. |
| --ctffile | str | Estimated CTF |