| --version |
None |
show program's version number and exit |
| --even |
str |
The filename of the map from the even 1/2 of the data |
| --odd |
str |
The filename of the map from the odd 1/2 of the data |
| --output |
str |
Filename for the final averaged/filtered result. |
| --compressbits |
int |
Bits to keep when writing (most) volumes with compression. 0->lossless floating point. Default 12 (3 significant figures) |
| --mass |
float |
The rough mass of the particle in kilodaltons, used to run normalize.bymass. Due to resolution effects, not always the true mass. |
| --restarget |
float |
The specified target resolution to avoid underfiltering artifacts. |
| --setsf |
str |
Force the structure factor to match a 'known' curve prior to postprocessing (<filename>, none). default=none |
| --iter |
int |
Iteration number to generate FSC filenames |
| --align |
None |
Will do o to e alignment and test for handedness flips. Should not be repeated as it overwrites the odd file with the aligned result. |
| --tomo |
None |
Modifies settings to be more appropriate for typical subtomogram averaging |
| --tophat |
str |
'global', 'local' or 'localwiener'. Overall Wiener filter disabled, and replaced by a tophat filter either across the map at 0.143 as Relion appears to do, or locally based on e2fsc_local_real.py results (either local tophat or local wiener) |
| --ampcorrect |
None |
Will perform amplitude correction via the specified method. The default choice is strucfac. |
| --ncmult |
float |
Specify how much to multiply noise cutoff during flattening amplitude correction. Default is 1.05. |
| --localsize |
float |
Override the automatic local region size (in A) used for local resolution calculation and filtration. |
| --m3dpostprocess |
str |
Default=none. An arbitrary post-processor to run after all other automatic processing. |
| --ppid |
int |
Set the PID of the parent process, used for cross platform PPID |
| --automaskexpand |
int |
Default=boxsize/20. Specify number of voxels to expand mask before soft edge. Only used if automask3d not specified. |
| --automask3d |
str |
Default=auto. Specify as a processor, eg - mask.auto3d:threshold=1.1:radius=30:nshells=5:nshellsgauss=5. |
| --mask |
str |
specify a density map file to use as mask. overwrites automask3d |
| --mergelowres |
float |
merge low resolution information of the two subset. |
| --automask3d2 |
str |
Default=None. Specify as a processor. This will be applied to the mask produced by the first automask. |
| --underfilter |
None |
This will shift the computed Wiener filter to be about 10%% more resolution than has been achieved. |
| --sym |
str |
Symmetry so we can decide how to align the particle. |
| --threads |
int |
Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful |