| --version |
None |
show program's version number and exit |
| --ref |
None |
3D reference for iterative alignment/averaging. <name> or <name>,#. For multiple references use this option multiple times. The first reference will be used for alignment. |
| --mask |
str |
Mask file to be applied to initial model |
| --maskalign |
str |
Mask file applied to 3D alignment reference in each iteration. Not applied to the average, which will follow normal masking routine. |
| --maskclass |
str |
Mask file applied to 3D classification references in each iteration. Not applied to the average. |
| --niter |
int |
Number of iterations |
| --sym |
str |
symmetry |
| --setsf |
str |
structure factor |
| --maxtilt |
float |
Explicitly zeroes data beyond specified tilt angle. Assumes tilt axis exactly on Y and zero tilt in X-Y plane. Default 90 (no limit). |
| --restarget |
float |
Filters each map at the end of each iteration to this resolution (in A) since FSC isn't available |
| --path |
str |
Specify name of refinement folder. Default is spt_XX. |
| --maxang |
float |
maximum anglular difference in refine mode. |
| --maxshift |
float |
maximum shift in pixel. |
| --ppid |
int |
Set the PID of the parent process, used for cross platform PPID |
| --threads |
int |
threads |
| --parallel |
str |
Thread/mpi parallelism to use |
| --transonly |
None |
translational alignment only |
| --refine |
None |
local refinement from xform in header. |
| --randphi |
None |
randomize phi for refine search |
| --rand180 |
None |
include 180 degree rotation for refine search |
| --scipy |
None |
test scipy refinement |