Particle Coordinates: Generate files containing particle coordinates for all input micrographs by picking particles manual and/or automatically.

Usage in command line

e2boxer_old.py  input_micrograph_list  --boxsize=BOXSIZE  --write_dbbox  --write_ptcls  --exclude_edges  --force  --format=FORMAT  --norm=NORM  --invert  --suffix=SUFFIX  --dbls=DBLS  --autoboxer=AUTOBOXER  --ppid=PPID  --gui  --verbose=n  --gauss_autoboxer=GAUSS_AUTOBOXER  --do_ctf=DO_CTF  --cter  --indir=INDIR  --nameroot=NAMEROOT  --micsuffix=MICSUFFIX  --wn=WN  --Cs=CS  --voltage=VOLTAGE  --ac=AC  --kboot=KBOOT  --debug  --apix=APIX

e2boxer_old exists in non-MPI version.

Start the e2boxer_old GUI with a list of micrographs:

e2boxer_old.py micrographs_number*

input_micrograph_list

Input micrographs: Wild cards (e.g. *) can be used to specify a list of micrographs. Not recommended if their number is very large. (default required string)

--boxsize

Box size [Pixels]: Box size for extraction of particle images. (default -1)

--write_dbbox

Write coordinate files: Write coordinate files. (default False)

--write_ptcls

Write particle images: Write particle images. (default False)

--exclude_edges

Exclude edge images: Exclude particles extending outside the micrograph. (default False)

--force

Force overwrite: Force overwrite. (default False)

--format

Particle image format: Format of the output particles images. (default hdf)

--norm

Particle normalization: Normalization processor applied to the final particle images. (default normalize.edgemean)

--invert

Invert contrast: Invert contrast of micrographs. (default False)

--suffix

Particle name suffix: Suffix used for the name of the output images and coordinates. (default _ptcls)

--dbls

Data base list storage: Data base list storage, used by the workflow. (default none)

--autoboxer

Swarm_boxers dict key: A key of the swarm_boxers dict in the local directory, used by the workflow. (default none)

--ppid

Set PPID: Sets the PPID of the process. (default -1)

--gui

Dummy option: Dummy option used in even older version of e2boxer_old. (default True)

--verbose

Verbose: Verbose level. Accepted values 0-9. (default 0)

--gauss_autoboxer

Sample autoboxed image: Gets the parameters used for autoboxing from the EMANDB. It requires the name of a micrograph used for automatic boxing previously. (default none)

--do_ctf

CTF parameters file: Specify name of file whose CTF estimation parameters should be used for automatic CTF estimation. (default none)

--cter

Use CTER CTF estimation: CTF estimation using CTER. (default False)

--indir

Input directory: Directory containing micrographs to be processed. (default current directory)

--nameroot

Micrograph rootname: Rootname of micrographs to be processed. (default none)

--micsuffix

Micrograph type: A string denoting micrograph type. (default none)

--wn

Window size: size of window to use. (default 256)

--Cs

Spherical aberration [mm]: Spherical aberration [mm] used to acquire the input micrographs. (default 2.0)

--voltage

Microscope voltage [kV]: Microscope voltage [kV] used to acquire the input micrographs. (default 300.0)

--ac

Amplitude contrast: Expected amplitude contrast of this dataset. (default 10.0)

--kboot

kboot: The number of boot-strap trials. (default 16)

--debug

Debug mode: Use debug mode. (default False)

--apix

Pixel size [A]: Pixel size of the input micrographs. (default -1.0)

The program creates the directory automatically in the micrograph directory.

EMAN2 Group

Category 1:: APPLICATIONS

programs/e2boxer_old.py

e2boxer and e2boxer FAQ

There are no known bugs so far.