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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: | + | ; %%--%%limit_resol_estep : to limit the resolution |
; %%--%%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 | + | |
+ | ; %%--%%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) | ||
+ | | ||
+ | ; %%--%%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 | + | ; bdb:3dclassified_stack |
; 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. |