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Options

Table 4.3: e2boxer.py Options
Argument Description
   
-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
   


next up previous contents index
Next: e2cmmtomrc.py Up: e2boxer.py Previous: Description   Contents   Index
2013-06-11