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pipeline:meridien:sp_higher_ord_abber

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pipeline:meridien:sp_higher_ord_abber [2021/03/16 10:58]
aali 		pipeline:meridien:sp_higher_ord_abber [2021/03/16 11:29]
aali
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 === Main Parameters === === Main Parameters ===
  
-  ; post_refine_folder : 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 : 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 : 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 (anisotropic) magnification  : Estimate magnification of dataset . (default False) +  ; %%--%%estimate_magnification :  Estimate magnification of dataset . (default False) 
-  ; %%--%%estimate_beamtilt : Estimate beamtilt : Estimate beamtilt from the dataset. (default False)  +  ; %%--%%estimate_beamtilt :  Estimate beamtilt from the dataset. (default False)  
-  ; %%--%%estimate_trefoil : Also estimate trefoil : estimate 3-fold astigmatism per optics group .(default False)  +  ; %%--%%estimate_trefoil : estimate 3-fold astigmatism per optics group .(default False)  
-  ; %%--%%estimate_order_aberation : Estimate the 4th order aberrations  :  Estimate the 4th order aberation .(default False)  +  ; %%--%%estimate_order_aberation : Estimate the 4th order aberation .(default False)  
-  ; %%--%%perform_CTF_params_fit : Perform CTF parameter fitting : Perform CTF parameter fitting. (default False) +  ; %%--%%perform_CTF_params_fit :  Perform CTF parameter fitting. (default False) 
-  ; %%--%%fit_defocus_micrograph : Fit defocus based on micrographs : Fit defocus based on micrographs. (default False)  +  ; %%--%%fit_defocus_micrograph : Fit defocus based on micrographs. (default False)  
-  ; %%--%%fit_defocus_particle : Fit defocus based on particles : Fit defocus based on particles. (default False)  +  ; %%--%%fit_defocus_particle : Fit defocus based on particles. (default False)  
-  ; %%--%%fit_astigmatism_micrograph :  Fit astigmatism based on micrographs : Fit astigmatism based on micrographs .(default False)  +  ; %%--%%fit_astigmatism_micrograph : Fit astigmatism based on micrographs .(default False)  
-  ; %%--%%fit_astigmatism_particle : Fit astigmatism based on particles : Fit astigmatism based on particles. (default False)  +  ; %%--%%fit_astigmatism_particle : Fit astigmatism based on particles. (default False)  
-  ; %%--%%fit_bfactor_micrograph : Fit bfactor based on micrographs : Fit bfactor based on micrographs. (default False) +  ; %%--%%fit_bfactor_micrograph : Fit bfactor based on micrographs. (default False) 
-  ; %%--%%fit_bfactor_particle : Fit bfactor based on particles : Fit bfactor based on particles. (default False) +  ; %%--%%fit_bfactor_particle :  Fit bfactor based on particles. (default False) 
-  ; %%--%%fit_phase_shift_micrograph : Fit phase shift estimation for micrographs : Fit phase shift estimation for micrographs .(default False)  +  ; %%--%%fit_phase_shift_micrograph :  Fit phase shift estimation for micrographs .(default False)  
-  ; %%--%%fit_phase_shift_particle : Fit phase shift estimation for particles : Fit phase shift estimation for particles. (default False)  +  ; %%--%%fit_phase_shift_particle :  Fit phase shift estimation for particles. (default False)  
-  ; %%--%%min_res_fit : minimum resolution value for fitting (A) : minimum resolution value for fitting (default 30.0)+  ; %%--%%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_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)   ; %%--%%submission_command : Submission commmand for cluster (default sbatch)
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 ===== Output ===== ===== Output =====
-  ; particles_ctf_refine.star : Output star file for polishing particles.+  ; particles_ctf_refine.star : Output star file for ctf refined stack.
   ; bdb:ctfrefine_stack : : Ctf refined particles stack. (still in test phase)   ; 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.   ; 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.
pipeline/meridien/sp_higher_ord_abber.txt · Last modified: 2021/03/22 16:49 by aali

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