RELION to SPHIRE Conversion: Create several types of parameter text files and per-micrograph virtual stacks of particle images in bdb format from parameters stored in a RELION STAR file

Usage in command line

sxrelion2sphire.py  input_star_file  output_directory  --relion_project_dir=DIR_PATH  --star_section=STAR_SECTION  --outputs_root=ROOT_NAME_STRING   --box_size=BOX_SIZE  --create_stack  --cs_save_as_hdf

sxrelion2sphire does not support MPI.

sxrelion2sphire.py  'Particles.star'  'Sphire_Project'  --box_size=256  --create_stack

sxrelion2sphire.py  'Refine3D/run1_data.star' 'Sphire_Project'  --star_section='data_images'  --box_size=100  --create_stack

sxrelion2sphire.py  'Relion_Project/Refine3D/run1_data.star'  'Sphire_Project'  --relion_project_dir='Relion_Project' --outputs_root='my_protein'  --create_stack

input_star_file

Input RELION STAR file: Specify a STAR file generated by RELION. The file should contain parameters related to Micrographs, CTF Estimation, Particle Extraction, 3D Alignment, or/and Random Subset. Entries for Micrographs category are required. If some entries associated with CTF Estimation, Particle Extraction, 3D Alignment, or/and Random Subset are missing, then the script does not produced the related output file(s). (default required string)

output_directory

Output directory: All the results will be written in here. It cannot be an existing one. (default required string)

--relion_project_dir

RELION project directory: Path to RELION project directory associated with the RELION STAR file. By default, the program assume the current directory is the RELION project directory. (default none)

--star_section

Section title in STAR file: The section title in the RELION star file where the data should be extracted. (default data_)

--outputs_root

Root name of outputs: Specify the root name of all outputs. It cannot be empty string or only white spaces. (default sphire)

--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 SPHIRE format is particle center. By default, use SPHIRE format. (default 0)

--create_stack

Create virtual stacks: Create per-micrograph virtual stacks of particle images in bdb format. By default, the program does not generate the stack of particle images because it takes a long time and the file size is large. (default False)

--cs_save_as_hdf

Save stack as HDF file: Save a stack file in HDF file format instead in bdb format. In this case, the stack file will contain all particle images in the input RELION STAR file. Effective only with --create_stack. (default False)

The program copies the subdirectory structure under the RELION project directory based on the information stored in the input RELION STAR file. For example, if two sets of micrographs are stored in two different subdirectories (e.g. “EM_Session01” and “EM_Session02” under a root micrograph directory (e.g. “Micrograph”), the program creates two subdirectories under the user-specified output directory (e.g. “Sphire_Project/EM_Session01” and “Sphire_Project/EM_Session02”). Each output subdirectory will contain the files in the table below.

Run the script to create several types of parameter text files and particle image stack in SPHIRE format from parameters stored in a RELION STAR file. The RELION STAR should contain entries related to Micrographs, CTF Estimation, Particle Extraction, 3D Alignment, or/and Random Subset. The entries for Micrographs category are required. If it does not contain some parameters associated with CTF Estimation, Particle Extraction, 3D Alignment, or/and Random Subset, then the command does not produce the related output file(s).

The following RELION STAR file entries are necessary to extract information for certain categories. The entries can exist in the file but won't be used by this command.

The script sets the following header entries of EMAN2DB/*_stack.bdb or *_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).

1. Change default stack format from HDF to bdb (--cs_save_as_hdf).
   • By default, the script creates a local particle image stack for each micrograph like sxwindow.py.
   • Likewise, because of synchronisation problem of subprocess execution, user must run particle stack command to create a virtual stack of all particles.
2. Accept arbitrary output file name (--outputs_root).

1. Added SPHIRE rebox file output support. The rebox file contains box coordinates, CTF parameters, and projection parameters.
   • This modification solves the problem associated with per-particle defocus estimation.

1. Add relion project directory option so that the script can be run from any directory (--relion_project_dir).

• That is, you don't anymore need to make sure the current directory is the project folder of the RELION (where you run RELION GUI).
• The program appends the path of relion project directory to micrograph path extracted from the star file.

These changes require user not to break the relative path whenever they move or copy the micrographs because sxrelion2sparx.py use full name including the path stored in the input RELION STAR file.

The program does not generate the following output files anymore.

To create these files, please use sxheader to extract information from the output stack or rewindowed stack with the output SPHIRE rebox files using sxrewindow.

Toshio Moriya

Category 1:: APPLICATIONS

sparx/bin/sxrelion2sphire.py

sxcter, sxgui_cter, sxwindow, sxrewindow, sxheader, sxpipe organize_micrographs, sxunblur, and sxsummovie.

Beta:: Under evaluation and testing. Please let us know if there are any bugs.

There are no known bugs so far.