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pipeline:meridien:sp_polishing

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pipeline:meridien:sp_polishing [2021/03/16 10:29]
aali [Output] 		pipeline:meridien:sp_polishing [2021/03/16 10:44]
aali [Usage]
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 ===== sp_polishing ===== ===== sp_polishing =====
  
-Bayesian : Apply Relion Bayesian Polishing on SPHIRE generated stack.+Bayesian Polishing : Apply Relion Bayesian Polishing on SPHIRE generated stack.
  
 ===== Usage ===== ===== Usage =====
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 <code> <code>
-sp_polishing.py post_refine_folder motioncorr_starfile output_folder training_params –first_frame +  sp_polishing.py post_refine_folder motioncorr_starfile output_folder training_params --first_frame --last_frame --bfac_minfreq --bfac_maxfreq --min_no_particles --submission_template --submission_command --relion_mpirun_executable --relion_polishing_executable --mpi_procs --no_of_threads --mrc_reloc_folder
-–last_frame –bfac_minfreq –bfac_maxfreq –min_no_particles –submission_template –submission_command +
-–relion_mpirun_executable –relion_polishing_executable –mpi_procs –no_of_threads –mrc_reloc_folder+
  
 </code> </code>
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 ===== Output ===== ===== Output =====
-shiny.star : Output star file for polishing particles. +  ; shiny.star : Output star file for polishing particles. 
-; ; bdb:polished_stack : : Polished particles stack. +  ; bdb:polished_stack : : Polished particles stack. 
-BDB2STAR : Using sphire2relion tool , the bdb stack is converted to star file so that it can be used in relion. The star file is saved in BDB2STAR folder. +  ; BDB2STAR : Using sphire2relion tool , the bdb stack is converted to star file so that it can be used in relion. The star file is saved in BDB2STAR folder. 
-PostProcess : Since the input to the tool is Post refiner directory, the tool can automatically create the necessary file in PostProcess folder which is necessary to provide for polishing.+  ; PostProcess : Since the input to the tool is Post refiner directory, the tool can automatically create the necessary file in PostProcess folder which is necessary to provide for polishing.
  
 =====   ===== =====   =====
pipeline/meridien/sp_polishing.txt · Last modified: 2021/03/16 10:44 by aali

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