Option Type Description
--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