| --version |
None |
show program's version number and exit |
| --ptclin |
str |
particle input |
| --ptclout |
str |
particle output |
| --ref |
str |
reference input |
| --threedout |
str |
map output |
| --keep |
float |
propotion of tilts to keep. default is 0.5 |
| --threads |
int |
Number of CPU threads to use. Default is 12. |
| --parallel |
str |
Thread/mpi parallelism to use. Default is thread:12 |
| --debug |
None |
Turn on debug mode. This will only process a small subset of the data (threads * 8 particles) |
| --transonly |
None |
only refine translation |
| --savepath |
None |
save alignment path in a json file for testing. |
| --fromscratch |
None |
align from scratch and ignore previous particle transforms. for spt mostly. will include mirror |
| --refineastep |
float |
Mean angular variation for refine alignment |
| --refinentry |
int |
number of starting points for refine alignment |
| --maxshift |
int |
maximum shift allowed |
| --localrefine |
None |
local refinement |
| --defocus |
None |
refine defocus. Still under development |
| --seedmap |
None |
seed |
| --ctfweight |
None |
weight by ctf |
| --skipm3d |
None |
skip make3d. only output aligned list |
| --padby |
float |
pad by factor. default is 2 |
| --maxres |
float |
max resolution for cmp |
| --minres |
float |
min resolution for cmp |
| --sym |
str |
symmetry. will use symmetry from spt refinement by default |
| --smooth |
int |
Smooth trajectory per image based on nearby particles. Still under development |
| --ppid |
int |
ppid... |
| --nkeep |
int |
|
| --verbose, -v |
int |
Verbose |