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## sp_higher_ord_abber

CTF Refinement : Apply relion ctf refinement for higher order aberration correction.

## Usage

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


## Typical usage

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).


## Input

#### Main Parameters

post_refine_folder
: Input folder is the directory where the results of the post refiner are present and python routine automatically locates all the required files used for ctf refinement. (default required string)
output_folder
: Output folder is the directory where all the results of the ctf refinement are saved. (default required string)
--estimate_magnification
Estimate magnification of dataset . (default False)
--estimate_beamtilt
Estimate beamtilt from the dataset. (default False)
--estimate_trefoil
estimate 3-fold astigmatism per optics group .(default False)
--estimate_order_aberation
Estimate the 4th order aberation .(default False)
--perform_CTF_params_fit
Perform CTF parameter fitting. (default False)
--fit_defocus_micrograph
Fit defocus based on micrographs. (default False)
--fit_defocus_particle
Fit defocus based on particles. (default False)
--fit_astigmatism_micrograph
Fit astigmatism based on micrographs .(default False)
--fit_astigmatism_particle
Fit astigmatism based on particles. (default False)
--fit_bfactor_micrograph
Fit bfactor based on micrographs. (default False)
--fit_bfactor_particle
Fit bfactor based on particles. (default False)
--fit_phase_shift_micrograph
Fit phase shift estimation for micrographs .(default False)
--fit_phase_shift_particle
Fit phase shift estimation for particles. (default False)
--min_res_fit
minimum resolution value for fitting (default 30.0)
--submission_template
Submission template for MPI command. In case of running this tool on a cluster, always a submission template. The number of MPI processors and threads in the submission template should be the same as the one specified below in the MPI procs and threads value.(default none)
--submission_command
Submission commmand for cluster (default sbatch)
--relion_mpirun_executable
Since there can be more than one mpirun environment installed on a workstation or on a cluster. It can be sometimes necessary to provide the relion specific mpirun executable. Just type which mpirun -a in a terminal and choose the one which relion requires. (default mpirun)
--relion_ctfrefine_executable
Similar to the issue of relion mpirun executable, it can be sometime necessary to provide the specific relion polishing executable also. Just type which relion_ctf_refine_mpi and copy the path here. (default relion_ctf_refine_mpi)
--mpi_procs
The number of MPI processors used for Relion multiprocessing. For training part only one MPI processors is used. In case when running the program on cluster, the MPI processors value should be same as used in the submission template.(default 1)
The number of threads use during the polishing. In case when running the program on cluster, the thread value should be same as used in the submission template.(default 1)

--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)

## Output

particles_ctf_refine.star
Output star file for ctf refined stack.
bdb:ctfrefine_stack
Ctf refined particles stack. (still in test phase, use relion2sphire for the time being)
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).



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.

## Description

### Reference

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.

### Developer Notes

Apply relion ctf refinement for higher order aberration correction

### Keywords

Category 1:: APPLICATIONS

### Files

sphire/bin/sp_higher_ord_abber.py