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pipeline:meridien:sp_higher_ord_abber [2021/03/16 11:29] aali |
pipeline:meridien:sp_higher_ord_abber [2021/03/22 16:40] aali |
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: The SPHIRE module provides a wrapper around the ctf refinement command. | : 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). | + | : 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 ===== | ===== Input ===== | ||
+ | |||
=== Main Parameters === | === 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) | + | ; post_refine_folder |
- | ; output_folder : Output folder is the directory where all the results of the ctf refinement are saved. (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) | + | ; < |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
- | | + | ; ; < |
===== Output ===== | ===== Output ===== | ||
- | | + | |
- | ; bdb: | + | ; ; particles_ctf_refine.star |
- | ; 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. | + | ; ; bdb: |
- | ; 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. | + | ; ; BDB2STAR |
+ | ; ; PostProcess | ||
===== ===== | ===== ===== | ||
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< | < | ||
- | module unload sphire (unload the module sphire) | + | module unload sphire (unload the module sphire) |
- | module load sphire/ | + | module load sphire/ |
module load relion | module load relion |