Name

sxrelion2sparx.py - creates several types of parameter text files and a particle image stack in SPARX format from parameters stored in a RELION STAR file

Usage

sxrelion2sparx.py input_star_file --output_dir=output_dir --star_section=star_section --box_size=box_size --create_stack

Input

Input star file containing Particle Extraction, 3D Alignment, CTF, and Random Subset parameters of each particle. Particle Extraction parameters are required. If it does not contain some parameters associated with 3D Alignment, CTF, or Random Subset, then the script does not produced the related output file(s).

Output

sparx_stack.hdf : Particle image stack (only when --create_stack option is used).

Coordinates/*.box : Coordinates files. One for each micrograph. It can be used as an input of sxwindow.

sparx_cter.txt : List of CTF parameters in cter format. It can be used as an input of sxwindow.

sparx_stack_ctf.txt : List of CTF parameters. It can be used as an input of sxheader --params=ctf.

sparx_stack_proj3d.txt : List of 3D projection parameters. It can be used as an input of sxheader --params=xform.projection.

sparx_stack_chunk0.txt : List of particle IDs for the subset #0. It can be used as an input of sxheader --params=chunk_id.

sparx_stack_chunk1.txt : List of particle IDs for the subset #1. It can be used as an input of sxheader --params=chunk_id.

Options

--output_dir=OUTPUT_DIR
output directory path.
--star_section=STAR_SECTION
section title in the RELION star file where data should be extracted. (default: 'data_')
--box_size=BOX_SIZE

Box size for particle extraction. It also controls the saved coordinates file format. If the given value is > 0, store the eman1 format. coordinate file. The coordinates of eman1 format is particle box corner associated with this box size. The coordinates of sparx format is particle center. (Default 0: use sparx format)

--create_stack
create particle stack. (default: False)

Description

== Typical usage ==

Run the script to create several types of parameter text files and particle image stack. Make sure the current directory is the project folder of the RELION (where you run RELION GUI).

The script adds and sets the following header entries of sparx_stack.hdf

NOTE: If you run sxwindow using the coordinates files generated by this script, ptcl_source_coord_id will be reassigned. It can be different from the RELION's local particle ID (the number before '@' in ptcl_source_relion).

Author / Maintainer

Toshio Moriya and Pawel A. Penczek

Keywords

category 1
APPLICATIONS

Files

sxrelion2sparx.py

See also

sxheader sxwindow

Maturity

alpha
in development

Bugs

None.

sxrelion2sparx (last edited 2015-12-07 17:30:54 by penczek)