Reboxing: Generate coordinates files and micrograph selection text file based on information stored in the image headers of SPHIRE particle stack file, by extracting coordinates from the input stack, then center them according to projection parameters in the header and user-provided 3D shift.

Usage in command line

sxpipe.py  reboxing  input_stack_path  output_directory  --box_size=BOX_SIZE  --shift3d_x=SHIFT3D_X  --shift3d_y=SHIFT3D_Y  --shift3d_z=SHIFT3D_Z

sxpipe reboxing does not support MPI.

sxpipe.py reboxing 'bdb:outdir_window#data' 'outdir_pipe_reboxing'  --box_size=352  --shift3d_z=15

input_stack_path

Input image stack: Specify path to input particle stack. (default required string)

output_directory

Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)

--box_size

Particle box size [Pixels]: The x and y dimensions of square area to be windowed. (default 0)

--shift3d_x

3D x-shift [Pixels]: User-provided 3D x-shift corresponding to shifting the 3D volume along x-axis. (default 0)

--shift3d_y

3D y-shift [Pixels]: User-provided 3D y-shift corresponding to shifting the 3D volume along y-axis. (default 0)

--shift3d_z

3D z-shift [Pixels]: User-provided 3D z-shift corresponding to shifting the 3D volume along z-axis. (default 0)

This command executes the following processes:

1. Extract the following information stored in the header of each particle image.
   • source micrograph path.
   • box center coordinates within the micrograph.
   • projection parameters.
2. Convert the center coordinates to EMAN1 box coordinates format, and then save the results to output files.
3. Transform the coordinates based on the projection parameters and user-provided 3D shift, and then save the results to output files.
4. Save the list of extracted micrograph names to an output file.

Wish list:

• Add --proj_params to use the projection parameter files stored in a text file instead of image headers.
• Setting --box_size to zero (default value) should save the coordinates file in SPHIRE format
• Save adjusted shifts to files
• Save projection parameters
• Save CTF parameters

Christos Gatsogiannis and Toshio Moriya

Category 1:: APPLICATIONS

sparx/bin/sxpipe.py

sxwindow, sxcter, sxgui_cter, sxwindow, sxpipe organize_micrographs, e2bdb

Alpha:: Under development.

There are no known bugs so far.