Bayesian Polishing : Apply Relion Bayesian Polishing on SPHIRE generated stack.
Usage in command line
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
sp_polishing exists in both MPI and non-MPI versions (Running MPI version does not require –MPI flag).
The purpose of sp_polishing.py is to :
: Apply Relion Bayesian Polishing using the stack generated from Meridien. : The SPHIRE module provides a wrapper around the polishing command for training as well motion estimation : After running the polishing routine, the wrapper automatically converts the shiny.star in the Output folder to a BDB stack and saves it in the folder name of Polish Stack.
To run it properly on cluster. Do the following task before running in case if you are running from MPI dortmund. These settings can be different if you are using it outside.
module unload sphire (unload the module sphire) module load sphire/clem/Polishing_SPHIRE_v1.2 or sphire/clr/Polishing_SPHIRE_v1.2 (this has to be done only in case if you have a different installation then the default one, since this tool is still not released, the git branch is different). module load relion
Then go to the directory where you have all the data folders. Like Meridien , Post Refiner, ISAC etc etc.
It is recommended to start SPHIRE in the folder structure where all the output folders are present e.g Post refinenment output folder, motioncorr output folder , ISAC substack output folder.
Jasenko Zivanov, Takanori Nakane and Sjors H W Scheres: A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis,
IUCrJ 6, 5-17, January, 2019..
Applying polishing using SPHIRE GUI.
Category 1:: APPLICATIONS
Beta:: Under evaluation and testing. Please let us know if there are any bugs.