| --version |
None |
show program's version number and exit |
| --path |
str |
Path to a folder where results should be stored, following standard naming conventions |
| --ref |
str |
reference map |
| --iter |
int |
Iteration number within path. Default = start a new iteration |
| --goldcontinue |
None |
Will use even/odd refs corresponding to specified reference to continue refining without phase randomizing again |
| --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) |
| --smooth |
float |
smooth local motion by this factor. smoother local motion with larger numbers. default 100 |
| --smoothN |
int |
number of neighboring particles used for smoothing. default 15 |
| --maxshift |
float |
max shift in pixel. default default box size/6 |
| --refine_trans |
None |
do translational alignment. |
| --refine_trans_ccf |
None |
do translational alignment using simple ccf. |
| --refine_rot |
None |
do translational-rotational alignment. better to start from an existing translational alignment. |
| --refine_defocus |
None |
do defocus refinement. need aliptcls input. doesn't work with refine_trans or rot yet.. |
| --use3d |
None |
use projection of 3d particles instead of 2d ones.. |
| --preprocess |
str |
Preprocess each 2-D subtilt while loading (alignment only) |
| --aliptcls2d |
str |
optional aliptcls input. the program can start search from the position from last run. |
| --aliptcls3d |
str |
optional aliptcls input. |
| --parallel |
str |
Thread/mpi parallelism to use |
| --debug |
None |
for testing. |
| --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 |