Table 4.3:
e2boxer.py Options
Argument |
Description |
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-version |
show program's version number and exit |
-h, -help |
show this help message and exit |
-gui |
Start the GUI for interactive boxing |
-B |
BOX, -box=BOX Box size in pixels |
-P |
PTCLSIZE, -ptclsize=PTCLSIZE Approximate size (diameter) of the particle in pixels. Not required if reference particles are provided. |
-R |
REFPTCL, -refptcl=REFPTCL A stack of reference images. Must have the same scale as the image being boxed. |
-V |
REFVOL, -refvol=REFVOL A 3D model to use as a reference for autoboxing |
-S |
SYM, -sym=SYM Symmetry of the 3D model |
-A |
AUTO, -auto=AUTO Autobox using specified method: circle, ref |
-T |
THRESHOLD, -threshold=THRESHOLD Threshold for keeping particles. 0-4, 0 excludes all, 4 keeps all. |
-nretest=NRETEST |
Number of reference images (starting with the first) to use in the final test for particle quality. |
-retestlist=RETESTLIST |
Comma separated list of image numbers for retest cycle |
-norm |
Edgenormalize boxed particles |
-savealiref |
Stores intermediate aligned particle images in boxali.hdf. Mainly for debugging. |
-farfocus=FARFOCUS |
filename or 'next', name of an aligned far from focus image for preliminary boxing |
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