pipeline:window:e2boxer

This version (2019/04/02 09:21) is a draft.
Approvals: 0/1

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


Usage in command line

e2boxer.py  input_micrograph_list  --apix=PIXEL_SIZE  --boxsize=BOX_SIZE  --ptclsize=PARTICLE_DIAMETER  --invert  --no_ctf  --gui  --write_dbbox  --allmicrographs  --unboxedonly  --write_ptcls  --suffix=SUFFIX  --voltage=VOLTAGE  --cs=CS  --ac=AMP_CONTRAST  --autopick=MODE  --threads=THREADS  --ppid=PPID  --verbose=LEVEL


e2boxer exists in non-MPI version.


Step 1: Use this command to start e2boxer's GUI with a list of micrographs using the right settings.

e2boxer.py CorrectedSums/corrsum_dose_filtered/*.mrc --apix=1.14 --boxsize=352 --invert --no_ctf --gui


Step 2: After user finished picking, run this command line to export .box files.

e2boxer.py CorrectedSums/corrsum_dose_filtered/*.mrc --apix=1.14 --boxsize=352 --invert --no_ctf --write_dbbox


Main Parameters

input_micrograph_list
Input micrograph list: Wild cards (e.g. *) can be used to specify a list of micrographs. Not recommended if their number is very large. (default required string)
--apix
Pixel size [A]: Angstroms per pixel for all images. (default -1)
--boxsize
Box size [Pixels]: Box size in pixels. (default -1)
--ptclsize
Particle diameter [Pixels]: Longest axis of particle in pixels (diameter, not radius). (default -1)
--invert
Invert input contrast: Preferably, particles should be brigt on a dark background. (default False)
--no_ctf
Disable CTF estimation: Disable CTF estimation. (default False)
--gui
Interactive GUI mode: Use interactive GUI mode. (default False)
--write_dbbox
Export EMAN1 box files: Export EMAN1 box files (.box extension). (default False)


Advanced Parameters

--unboxedonly
Include only unboxed micrographs: Only include image files without existing box locations. (default False)
--write_ptcls
Save selected particle: Extract selected particles from micrographs and write to disk. (default False)
--allmicrographs
Include all micrographs in a directory: Add all images from micrographs folder. (default False)
--suffix
Micrograph suffix: Suffix of the micrographs used for particle picking (i.e. suffix=goodali will use micrographs end with _goodali.hdf). It is only useful when –allmicrographs option is True. (default none): --allmicrographs==True
--voltage
Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default -1)
--cs
Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default -1)
--ac
Amplitude contrast [%]: The typical amplitude contrast is in the range of 7% - 14%. The value mainly depends on the thickness of the ice embedding the particles. (default 10.0)
--autopick
Perform automatic particle picking: Provide mode and parameter string (eg - auto_local:threshold=5.5). (default none)
--threads
Number of threads: Number of threads to run in parallel on a single computer. (default 4)
--ppid
Parent process PID: Set the PID of the parent process, used for cross platform PPID. (default -1)
--verbose
Use verbose mode: Specify verbose level [0-9]. Higner number means higher level of verboseness. (default 0)







EMAN2 Group


Category 1:: APPLICATIONS


programs/e2boxer.py


Beta:: Under development


  • pipeline/window/e2boxer.txt
  • Last modified: 2019/04/02 09:21
  • by lusnig