pipeline:utilities:sp_sphire2relion

This version (2019/04/02 12:34) is a draft.
Approvals: 0/1

SPHIRE to RELION Conversion : Convert SPHIRE parameters to RELION.


Usage in command line

sp_sphire2relion.py output_dir --output_name=OUTPUT_NAME --particle_stack=PARTICLE_STACK  --params_2d_file=PARAMS_2D_FILE --params_3d_file=PARAMS_3D_FILE -params_3d_index_file=PARAMS_3D_INDEX_FILE  --params_3d_chunk_file_0=CHUNKFILE0 --params_3d_chunk_file_1=CHUNKFILE1 --list=INCLUDE_LIST --exlist=EXCLUDE_LIST --force


Fill it.


Main Parameters

output_dir
Output directory: Output directory. (default required string)
--output_name
Output star file name: Output star file name. (default none)
--particle_stack
Particle stack: Particle stack in bdb or hdf format. (default none)
--params_2d_file
2D params file: 2D alignment parameters. (default none)
--particle_stack!=none --params_3d_file==none
--params_3d_file
3D params file: 3D projection parameters. (default none)
--particle_stack!=none --params_2d_file==none
--params_3d_index_file
3D params index file: Index file for the 3d params. Used to find the associated particle stack entry in the params file. In the meridien directories, this file is either called chunk or index.(default none)
--particle_stack!=none --params_3d_file!=none
--params_3d_chunk_file_0
First 3D params chunk file: First chunk file for the 3d params. Used to extract the _rlnRandomSubset information. In the meridien directories, this file is called chunk. (default none)
--particle_stack!=none --params_3d_file!=none
--params_3d_chunk_file_1
Second 3D params chunk file: Second chunk file for the 3d params. Used to extract the _rlnRandomSubset information. In the meridien directories, this file is called chunk. (default none)
--particle_stack!=none --params_3d_file!=none


Advanced Parameters

--force
Force: Overwrite existing star file. (default False))
--list
Include particle list: List of particles to include. Requires –particle_stack. Cannot be used together with –exlist. (default None)
--particle_stack!=None --exlist==None
--exlist
Exclude particle list: List of particles to exclude. Requires –particle_stack. Cannot be used together with –list. (default None)
--particle_stack!=None --list==None








Category 1:: APPLICATIONS


sparx/bin/sp_sphire2relion.py



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


There are no known bugs so far.


  • pipeline/utilities/sp_sphire2relion.txt
  • Last modified: 2019/04/02 12:34
  • by lusnig