usage: prog [options] <refine_xx folder> <iteration number> WARNING - particularly with a lot of threads and larger box-sizes, this program can eat a LOT of RAM. Try running on a small number of threads briefly, and monitor memory usage before ramping up to the full number of available threads. This program modifies raw particle data to subtract-away undesired portions of the density on a per-particle basis. For example, one could take GroEL particles with D7 symmetry and extract the top and bottom heptamers as separate particles for reconstruction. In this example there would be 2x as many output particles as input particles. The portion of the map identified by the excluded region mask will be subtracted from each particle as optimally as possible, taking CTF, normalization and other factors into account. To use this program you should first run a complete refinement to the best possible resolution. Refinement parameters will be examined automatically to extract the corresponding particles and projections. Since each input particle may possibly become multiple output particles (with --sym), no relationship to the original micrographs is maintained, and a single output stack is generated by this program.
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --sym | None | Specify symmetry - choices are: c<n>, d<n>, tet, oct, icos. If specified each input 'particle' will become N extracted subparticles. |
| --subunitmask | str | Required. When applied to the 3-D volume, this mask contains the subunit being extracted. 'soft' edges are permitted |
| --outermask | str | Optional. If specified, this mask is projected into 2-D and used to mask out noise outside the subunit. If not specified a thresholded subunitmask is used. Only useful with --masked. |
| --masked | None | If specified, each output subparticle will be masked based on the projection mask. Recommended. |
| --newbox | int | New box size for extracted regions |
| --invartype | None | Which type of invariants to generate: (bispec,harmonic) |
| --threads | int | Number of threads to run in parallel on a single computer |
| --verbose, -v | int | verbose level [0-9], higher number means higher level of verboseness |
| --debug | None | Enable debugging mode with verbose output and image display. Not suitable for real runs. |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |