Table 4.7:
e2make3d.py Options
| Argument |
Description |
| |
|
| -version |
show program's version number and exit |
| -h, -help |
show this help message and exit |
| -out=FILENAME |
Output 3D MRC file |
| -lowmem |
Read in images only when needed instead of preloading all in memory |
| -sym=SYM |
Set the symmetry; if no value is given then the model is assumed to have no symmetry. Choices are: i, c, d, t, icos, or oct |
| -pad=PAD |
To reduce Fourier artifacts, the model is typically padded by 25% |
| -mode=MODE |
Specifies the interpolation size (1 to 6), 2 is the default |
| -recon=RECON_TYPE |
Reconstructor to use |
| -quiet |
Quiet output |
| -snrfile=SNRFILE |
Use a SNR file (as generated by classalignall) for proper 3D Wiener filtration |
| -goodbad |
Saves the used and unused class averages in 2 files |
| -log |
Averages the log of the projections |
| -inorm |
This will use a special weighting scheme to compensate for poor SNR sampling on the unit sphere |
| -fftmerge=FFTMERGE |
Fourier model to merge with real model |
| -savenorm |
Saves the normalization map to norm.mrc |
| -hard=HARD |
This specifies how well the class averages must match the model to be included, 25 is typical |
| -noweight |
Normally the class averages are weighted by the number of raw particles used, this disables that |
| -mask=MASK |
Real-space mask radius |
| -apix=APIX |
Set the sampling (angstrom/pixel) |
| -keep=SIGM |
An alternative to 'hard' |
| -resmap=RESMAP |
Generates a 'resolution map' in another 3D MRC file |
| |
|