| --version |
None |
show program's version number and exit |
| --boxsize, -B |
int |
Box size in pixels |
| --write_dbbox |
None |
Write coordinate file (eman1 dbbox) files |
| --write_ptcls |
None |
Write particles to disk |
| --exclude_edges |
None |
Don't generate output for any particles extending outside the micrograph |
| --exclude_bad |
None |
Don't generate output for any particles marked as exclude |
| --force, -f |
None |
Force overwrite |
| --format |
None |
Format of the output particle images. For EMAN2 refinement must be HDF. |
| --norm |
str |
Normalization processor to apply to written particle images. Should be normalize, normalize.edgemean,etc.Specific "None" to turn this off |
| --invert |
None |
If writing outputt inverts pixel intensities |
| --suffix |
str |
suffix which is appended to the names of output particle and coordinate files |
| --dbls |
str |
data base list storage, used by the workflow. You can ignore this argument. |
| --autoboxer |
str |
A key of the swarm_boxers dict in the local directory, used by the workflow. |
| --ppid |
int |
Set the PID of the parent process, used for cross platform PPID |
| --gui |
None |
Dummy option; used in older version of e2boxer |
| --verbose, -v |
int |
verbose level [0-9], higher number means higher level of verboseness |
| --gauss_autoboxer |
str |
Name of autoboxed file whose autoboxing parameters (obtained via some previous run of Gauss autoboxer via the GUI) should be used for automatic boxing. |
| --do_ctf |
str |
Name of file whose ctf estimation parameters (obtained via some previous run of Gauss autoboxer via the GUI) should be used for automatic ctf estimation. |
| --cter |
None |
CTF estimation using cter |
| --indir |
str |
Directory containing micrographs to be processed. |
| --nameroot |
str |
Prefix of micrographs to be processed. |
| --micsuffix |
str |
A string denoting micrograph type. For example 'mrc', 'hdf', 'ser' ... |
| --wn |
int |
Size of window to use (should be slightly larger than particle box size) |
| --Cs |
float |
Microscope Cs (spherical aberation) |
| --voltage |
float |
Microscope voltage in KV |
| --ac |
float |
Amplitude contrast (percentage, default=10) |
| --kboot |
int |
kboot |
| --MPI |
None |
use MPI version |
| --debug |
None |
debug mode |
| --apix |
float |
pixel size in Angstroms |