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pipeline:meridien:sp_relion_3dclassifi

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pipeline:meridien:sp_relion_3dclassifi [2021/03/16 11:19]
aali created
pipeline:meridien:sp_relion_3dclassifi [2021/03/16 11:29]
aali
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   ; %%--%%diam_mas : The diameter of the mask (A) which use. (default 200)   ; %%--%%diam_mas : The diameter of the mask (A) which use. (default 200)
   ; %%--%%zeros_mas :  in case padding with zeros is required. (default True)    ; %%--%%zeros_mas :  in case padding with zeros is required. (default True) 
-  ; %%--%%limit_resol_estep: to limit the resolution  E-step to (A) for fitting (default -1)+  ; %%--%%limit_resol_estep : to limit the resolution  E-step to (A) for fitting (default -1)
   ; %%--%%heal_pix_order : Angular sampling interval in degrees. output value can be from 8 to 0 depends on selection of values from 0.1 to 30 degrees (default 7.5 ||| 0.1 ||| 0.2 ||| 0.5 ||| 0.9 ||| 1.8 ||| 3.7 ||| 15 ||| 30)   ; %%--%%heal_pix_order : Angular sampling interval in degrees. output value can be from 8 to 0 depends on selection of values from 0.1 to 30 degrees (default 7.5 ||| 0.1 ||| 0.2 ||| 0.5 ||| 0.9 ||| 1.8 ||| 3.7 ||| 15 ||| 30)
   ; %%--%%off_range : Offset search range (pix). Probabilities will be calculated only for translations in a circle with this radius in pixels. (default 5)   ; %%--%%off_range : Offset search range (pix). Probabilities will be calculated only for translations in a circle with this radius in pixels. (default 5)
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 === Advanced Parameters === === Advanced Parameters ===
  
-  ; %%--%%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)+  ; %%--%%abs_greyscale_map : Ref map is on absolute greyscale . Whether the reference map is on absolute greyscale level or not. (default False) 
 +  ; %%--%%use_fast_sets : Use fast subsets for large datasets . if selected the first 5 iterations will be done with random subsets of only K*1500 particles. (default False) 
 +  ; %%--%%skip_img_align : Skip image alignment . Whether to skip image alignment or not . (default False) 
 +  ; %%--%%ang_search : Perform local angular searches . Whether to perform angular search or not. (default False) 
 +  ; %%--%%ang_search_range : Local angular search range . in case if is set to Yes, value is multiplied by 0.33333. (default 5) : %%--%%ang_search==True 
 +  ; %%--%%ang_search_relax_sym : to relax symmetry . (default None) : %%--%%ang_search==True 
 +  ; %%--%%para_io : Use parallel disc I/O. (default True) 
 +  ; %%--%%skip_pad : depends on the answer for skip padding, if set to No , then pad is 2 , if set to yes then pad is 1. (default False) 
 +  ; %%--%%skip_grid :  Whether to skip the grid or not. (default True) 
 +  ; %%--%%pre_read_img : Pre-read all particles in memory. (default False) 
 +  ; %%--%%scratch_dir : Copy particles to search directory. if --preread_images is set to No and if a directory link is provided in Copy particles to scratch directory (default None) 
 +  ; %%--%%combine_iter_disc : Combine iterations through disc. Whether to combine iterations or not. (default False) 
 +  ; %%--%%mrc_reloc_folder : mrc relocation 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) 
 +  ; %%--%%helical_recons : Do helical reconstruction.(default False) 
 +  ; %%--%%inner_diam :  Helical tube inner diameter (A). (default -1)  
 +  ; %%--%%outer_diam : Helical tube outer diameter (A). (default -1)  
 +  ; %%--%%sig_tilt :  angular search range value in degrees for tilt. (default 15)  
 +  ; %%--%%sig_psi : angular search range value in degrees for psi. (default 10)  
 +  ; %%--%%sig_rot :  angular search range value in degrees for rot. (default -1)  
 +  ; %%--%%sigma_dist : Range factor of local averaging : Local averaging of orientations and translations will be performed within a range of +/- this value * the box size.(default 1.5)  
 +  ; %%--%%keep_tilt_fix :  Tilt prior will not change during the optimization. (default True) 
 + ; %%--%%apply_helical_sym : Whether to apply helical symmetry or not . (default False) 
 +  ; %%--%%unique_asym_unit : Number of unique asymmetrical units in each segment box. (default 1) 
 +  ; %%--%%initial_twist : Initial twist (deg) set to positive value if it is a right-handed helix. (default 0)  
 +  ; %%--%%initial_rise : Initial rise (A) set to positivie value .(default 0) 
 +  ; %%--%%z_percent : Central Z length (%) for information from the central part of the box is used for search and imposing helical symmetry in real space. (default 30)  
 +  ; %%--%%do_local_search : Peform local searches of helical twist and rise within given range . (default False) 
 +  ; %%--%%twist_min : Miniumum value for twist search (deg). Set it to a positive value if it is a right-handed helix. (default 0)  
 +  ; %%--%%twist_max : Maxiumum value for twist search (deg). (default 0) 
 +  ; %%--%%twist_inistep : Need to set manually set if the default value (deg) does not guarantee convergence. (default 0)  
 +  ; %%--%%rise_min : Rise search minimum value (A) . Set is to a positive value in angstorms. (default 0)  
 +  ; %%--%%rise_max : Rise search maxiumum value (A). (default 0) 
 +  ; %%--%%rise_inistep : Rise search initial step (A). Need to set manually set if the default value does not guarantee convergence. (default 0
  
 ===== Output ===== ===== Output =====
-  ; particles_ctf_refine.star : Output star file for polishing particles+  ; 3dstack.star : Output star file. 
-  ; bdb:ctfrefine_stack : : Ctf refined particles stack. (still in test phase)+  ; bdb:3dclassified_stack : : 3dclassified 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.
   ; 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.   ; 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.
pipeline/meridien/sp_relion_3dclassifi.txt · Last modified: 2021/03/16 11:33 by aali