| --version |
None |
show program's version number and exit |
| --reference, --ref |
None |
3D reference for iterative alignment/averaging. No reference is used by default. <name> or <name>,# |
| --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. |
| --niter |
int |
Number of iterations |
| --sym |
str |
symmetry |
| --maxres |
float |
Maximum resolution (the smaller number) to consider in alignment (in A, not 1/A) |
| --minres |
float |
Minimum resolution (the larger number) to consider in alignment (in A, not 1/A, default=200) |
| --mass |
float |
mass. default -1 will skip by mass normalization |
| --localfilter |
None |
Deprecated. Please use --tophat |
| --tophat |
str |
'local', 'localwiener' or 'global'. Instead of imposing a uniform Wiener filter, use a tophat filter (global similar to Relion). local is a local tophat filter, localwiener is a localized Wiener filter |
| --goldstandard |
int |
Phase randomization resolution for gold standard refinement in A. Not equivalent to restarget in e2refine_easy. |
| --goldcontinue |
None |
continue from an existing gold standard refinement |
| --restarget |
float |
The resolution you reasonably expect to achieve in the current refinement run in A. |
| --setsf |
str |
structure factor |
| --pkeep |
float |
fraction of particles to keep |
| --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). |
| --path |
str |
Specify name of refinement folder. Default is spt_XX. |
| --smooth |
float |
smoothing factor for subtlt. |
| --maxang |
float |
maximum anglular difference in refine mode. |
| --maxshift |
float |
maximum shift in pixel. |
| --threads |
int |
threads |
| --parallel |
str |
Thread/mpi parallelism to use |
| --transonly |
None |
translational alignment only |
| --refine |
None |
local refinement from xform in header. |
| --refinentry |
int |
Number of local perturbations to initialize local alignment with (default=8) |
| --realign |
None |
realigns the average to the initial reference to prevent drift in C1 refinements |
| --randphi |
None |
randomize phi for refine search |
| --rand180 |
None |
include 180 degree rotation for refine search |
| --test180 |
None |
Test for improved alignment with 180 degree rotations even during refine alignment |
| --resume |
None |
resume from previous run |
| --scipy |
None |
test scipy refinement |
| --breaksym |
None |
break symmetry |
| --breaksymsym |
str |
Specify a different symmetry for breaksym. |
| --symalimask |
str |
This will translationally realign each asymmetric unit to the previous map masked by the specified mask. While this invokes symalimasked in e2spt_average, this isn't the same, it is a mask, not a masked reference. |
| --ppid |
int |
Set the PID of the parent process, used for cross platform PPID |
| --verbose, -v |
int |
verbose level [0-9], higher number means higher level of verboseness |