pipeline:utilities:sp_sphire2relion

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pipeline:utilities:sp_sphire2relion [2019/04/02 12:34] (current)
lusnig created
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 +~~NOTOC~~
 +
 +===== sp_sphire2relion =====
 +SPHIRE to RELION Conversion : Convert SPHIRE parameters to RELION.
 +
 +\\
 +===== Usage =====
 +
 +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
 +\\
 +===== Typical usage =====
 +
 +Fill it.
 +
 +\\
 +===== Input =====
 +=== 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
 +
 +\\
 +===== Output =====
 + 
 +\\
 +===== Description =====
 +
 +\\
 +==== Method ====
 +
 +\\
 +==== Reference ====
 +
 +\\
 +==== Developer Notes ====
 +
 +\\
 +==== Author / Maintainer ====
 +
 +\\
 +==== Keywords ====
 +Category 1:: APPLICATIONS
 +
 +\\
 +==== Files ====
 +sparx/​bin/​sp_sphire2relion.py
 +
 +\\
 +==== See also ====
 +
 +\\
 +==== Maturity ====
 +Beta:: Under evaluation and testing. Please let us know if there are any bugs.
 +
 +\\
 +==== Bugs ====
 +There are no known bugs so far.
 +
 +\\
  
  • pipeline/utilities/sp_sphire2relion.txt
  • Last modified: 2019/04/02 12:34
  • by lusnig