Name

sxrelion2sparx.py - creates three 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 --create_stack

Input

Input star file containing CTF, 3D Alignment, and Random Subset parameters of each particle.

Output

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

sparx_params_ctf.txt : List of CTF parameters corresponding to "ctf"

sparx_params_proj3d.txt : List of 3D projection parameters corresponding to "xform.projection"

chunk1.txt : List of particle IDs belonging to the subset #1

chunk2.txt : List of particle IDs belonging to the subset #2

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_')

--create_stack

create particle stack (default: False)

Description

Typical usage

(1) Run the script to create CTF and 3D projection parameter text files and particle image stack. Make sure the current directory is the project folder of the RELION (where you run RELION GUI).

• sxrelion2sparx.py Refine3D/run1_data.star --output_dir=sparx_work --star_section=data_images --create_stack

(2) Manually import the parameters into the headers of your stack file.

• sxheader.py sparx_stack.hdf --params=ctf --import=sprax_stack_params_ctf.txt
• sxheader.py sparx_stack.hdf --params=xform.projection --import=sparx_stack_params_proj3d.txt

Author / Maintainer

Toshio Moriya and Pawel A. Penczek

Keywords

category 1

FUNDAMENTALS, UTILITIES, APPLICATIONS

Files

sxrelion2sparx.py

See also

sxheader

Maturity

alpha

in development

Bugs

None.