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===== sp_sphire2relion =====
SPHIRE to RELION Conversion : Convert SPHIRE parameters to RELION.

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===== Usage =====

Usage in command line

  sp_sphire2relion.py relion_project_dir output_directory --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
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===== Typical usage =====

Fill it.

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===== Input =====
=== Main Parameters ===
  ; output_directory : Output directory: Output directory containing the output star file. (default required string)
  ; %%--%%relion_project_dir : Relion project directory: Relion project directory. (default .)
  ; %%--%%output_name : Output star file name:  Output star file name. (default sphire2relion.star)
  ; %%--%%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



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=== 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

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===== Output =====
 
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===== Description =====

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==== Method ====

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==== Reference ====

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==== Developer Notes ====

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==== Author / Maintainer ====

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
sphire/bin/sp_sphire2relion.py

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==== See also ====

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

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==== Bugs ====
There are no known bugs so far.

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