| --version |
None |
show program's version number and exit |
| --path |
str |
Path to a folder where results should be stored, following standard naming conventions (default = spt_XX) |
| --iter |
int |
Iteration number within path. Default = 0 |
| --goldcontinue |
None |
Will use even/odd refs corresponding to specified reference to continue refining without phase randomizing again |
| --sym |
str |
Symmetry of the input. Must be aligned in standard orientation to work properly. |
| --maxres |
float |
Maximum resolution to consider in alignment (in A, not 1/A) |
| --minres |
float |
Minimum resolution to consider in alignment (in A, not 1/A) |
| --parallel |
str |
Thread/mpi parallelism to use |
| --fromscratch |
None |
Start from exhaustive coarse alignment. Otherwise will use alignment from the previous rounds and do local search only. |
| --use3d |
None |
use projection of 3d particles instead of 2d sub tilt series |
| --preprocess |
str |
Preprocess each 2-D subtilt while loading (alignment only) |
| --debug |
None |
Debug mode. Will run a small number of particles directly without parallelism with lots of print out. |
| --plst |
str |
list of 2d particle with alignment parameters. The program will reconstruct before alignment so it can be slower. |
| --maxshift |
int |
Maximum shift from the center of the box or the previous alignment. default box size//6 |
| --maxang |
int |
Maximum angle difference from starting point. Ignored when --fromscratch is on. |
| --curve |
None |
Mode for filament structure refinement. Still under testing. Ignored when --fromscratch is on. |
| --skipali |
None |
Skip alignment and only calculate the score. Incompatible with --fromscratch, but --breaksym will still be considered. |
| --breaksym |
str |
Specify symmetry to break. Ignored when --fromscratch is on. |
| --verbose, -v |
int |
verbose level [0-9], higher number means higher level of verboseness |
| --ppid |
int |
Set the PID of the parent process, used for cross platform PPID |