| --version |
None |
show program's version number and exit |
| --path |
str |
Output path, default=sptcls_XX |
| --ncls |
int |
Number of classes to generate. Specify this or multiple --ref options. Default 2 |
| --ref |
None |
3D reference for iterative alignment/averaging. <name> or <name>,#. For multiple references use this option multiple times. Refs autogenerated if this is not specified. |
| --niter |
int |
number of iterations |
| --maxres |
float |
max resolution in A |
| --parm |
str |
particle_parms_xx.json file from spt_refine, this provides both the input particles and alignment parameters |
| --strucfac |
str |
Structure factor file |
| --parallel |
str |
parallel |
| --mask |
str |
mask file |
| --sym |
str |
|
| --applysym |
str |
|
| --symcopy |
None |
Copy each particle for each asymetrical unit. need a maskclass to focus on one unit. do not work with applysym |
| --randsym |
None |
randomize symmetry unit assignment at the begining. seems to be helpful for high symmetry without obvious asymetrical features.. |