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CTF Refinement : Apply relion ctf refinement for higher order aberration correction.
Usage in command line
sp_higher_ord_abber.py post_refine_folder output_folder --estimate_magnification --estimate_beamtilt --estimate_trefoil --estimate_order_aberation --perform_CTF_params_fit --fit_defocus_micrograph --fit_defocus_particle --fit_astigmatism_micrograph --fit_astigmatism_particle --fit_bfactor_micrograph --fit_bfactor_particle --fit_phase_shift_micrograph --fit_phase_shift_particle --min_res_fit --submission_template --submission_command --relion_mpirun_executable --relion_ctfrefine_executable --mpi_procs --no_of_threads --mrc_reloc_folder
sp_higher_ord_abber exists in both MPI and non-MPI versions (Running MPI version does not require –MPI flag).
The purpose of sp_higher_ord_abber.py is to :
: Apply CTF refinement to estimation different parameters such beam tilt, phase shift, magnification etc. : The SPHIRE module provides a wrapper around the ctf refinement command. : After running the ctf refinement routine, the wrapper automatically converts the star file and apply beam tilt correction on the star2BDB converted stack so that it can be used directly for further processing. (still in test phase).
; ; --mrc_reloc_folder : : In case if the mrcs images were moved from original location where they were generated to a new location. Then the user has to provide a path directory link to the new location . (default none)
; ; particles_ctf_refine.star : : Output star file for ctf refined stack. ; ; bdb:ctfrefine_stack : : Ctf refined particles stack. (still in test phase) ; ; 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 ctf refinement.
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: Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1, IUCrJ
7, 253-267, March, 2020.
Apply relion ctf refinement for higher order aberration correction
Adnan Ali
Category 1:: APPLICATIONS
sphire/bin/sp_higher_ord_abber.py
Beta:: Under evaluation and testing. Please let us know if there are any bugs.