| --version |
None |
show program's version number and exit |
| --path |
str |
Path to the previous spt/subtlt refinement (required) |
| --iter |
int |
Start from iteration X of previous refinement |
| --niters |
int |
Run this many iterations. Default is 4. |
| --keep |
float |
propotion of tilts to keep. default is 0.8 |
| --maxalt |
float |
max altitude to insert to volume |
| --mask |
str |
Refinement and reprojection masking. Default uses mask from source |
| --maskalign |
str |
Mask to apply during alignment, but not the final model. Default is to use the same mask. |
| --nogs |
None |
Skip gold standard. This is not a great idea... |
| --threads |
int |
Number of CPU threads to use. Default is 12. |
| --parallel |
str |
Thread/mpi parallelism to use. Default is thread:12 |
| --buildsetonly |
None |
will only prepare particle set for the refinement but skip the actual refinement process. |
| --resume |
None |
continue from previous run |
| --reproject |
None |
Reproject 3D particles into 2D particles. |
| --reprj_offset |
str |
Offset translation before reprojection |
| --reprj_clip |
int |
clip after reprojection |
| --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 local Wiener filter |
| --refineastep |
float |
Mean angular variation for refine alignment |
| --refinentry |
int |
number of starting points for refine alignment |
| --maxshift |
int |
maximum shift allowed |
| --padby |
float |
pad by factor. default is 1.5 |
| --debug |
None |
Turn on debug mode. This will only process a small subset of the data (threads * 8 particles) |
| --localnorm |
None |
local normalization. do not use yet.... |
| --sym |
str |
symmetry. will use symmetry from spt refinement by default |
| --ppid |
int |
ppid... |
| --transonly |
None |
only refine translation |
| --maxres |
float |
max resolution for fsc |
| --minres |
float |
min resolution for fsc |