| --version |
None |
show program's version number and exit |
| --ptcl |
str |
Input particle stack. |
| --ref |
str |
Reference map. This will be scaled/clipped to match the particles automatically. |
| --path |
str |
Path for refinement output files. default is r3d_xx |
| --parallel |
str |
Run in parallel, specify type:<option>=<value>:<option>=<value>. |
| --sym |
str |
sym |
| --res |
float |
The resolution that reference map is lowpass filtered to (with phase randomization) at the begining of the refinement. |
| --keep |
float |
Fraction of best particles to keep in each iteration. |
| --niter |
int |
Number of iterations. Default is 10. |
| --startiter |
int |
Start from a specified iteration in an existing refinement |
| --setsf |
str |
Text file containing structure factor for map sharpening. Can be produced during CTF estimation, or from an existing high resolution map. |
| --tophat |
str |
Options for filtering maps. Run 'e2help.py tophat' for more information. Default=local. |
| --threads |
int |
Threads to use during postprocessing of 3d volumes |
| --mask |
str |
Specify a mask file for each iteration of refinement. Otherwise will generate mask automatically. |
| --compressbits |
int |
Bits to keep when writing images. 4 generally safe for raw data. 0-> true lossless (floating point). Default 6 |
| --localsize |
float |
Override the automatic local region size (in A) used for local resolution calculation and filtration. |
| --m3dthread |
None |
do make3d in threading mode with shared memory. safer for large boxes |
| --verbose, -v |
int |
verbose level [0-9], higher number means higher level of verboseness |