| --output |
None |
Output reconstructed volume file name. |
| --input |
None |
The input projections. Project should usually have the xform.projection header attribute, which is used for slice insertion |
| --sym |
None |
Set the symmetry; if no value is given then the model is assumed to have no symmetry.\nChoices are: i, c, d, tet, icos, or oct. |
| --pad |
int |
Will zero-pad images to the specifed size. |
| --outsize |
int |
Defines the dimensions of the final volume written to disk |
| --keep |
str |
The fraction of slices to keep, based on quality scores (1.0 = use all slices). |
| --no_wt |
None |
This argument turns automatic weighting off causing all images to be weighted by 1. |
| --mode |
str |
Fourier reconstruction 'mode' to use. The default should not normally be changed. |
| --verbose, -v |
int |
verbose level [0-9], higher number means higher level of verboseness |
| --apix |
float |
A/pix value for output, overrides automatic values |
| --tidrange |
str |
Range of tilt id to include for particles from tilt series. Specify two integers separated by ','. |
| --ref |
str |
Weight each particle using a specified reference map. |
| --minres |
float |
minimum resolution to compare when weighting by a reference map. |
| --maxres |
float |
maximum resolution to compare when weighting by a reference map. |
| --parallel |
str |
Thread/mpi parallelism to use without shared memory. Each worker will reconstruct a map with a subset of particles and the results from workers will be averaged together with the corresponding Fourier weighting. Along with --threads, this allows having one worker per node using multiple threads. |
| --threads |
int |
Number of threads using shared memory. |
| --setsf |
str |
Set structure factor from text file |
| --debug |
None |
Turn on debug mode. This will only process a small subset of the data. |
| --clsid |
str |
Only reconstruct a class of particles. Also take even/odd to reconstruct subsets of particles. |
| --listsel |
str |
only reconstruct particles of indices from the given list in a text file. |
| --p3did |
int |
only reconstruct images for one 3d particle of the given ID. |
| --ppid |
int |
Set the PID of the parent process, used for cross platform PPID |