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pipeline:sort3d:sxsort3d [2018/02/23 16:59]
moriya 		pipeline:sort3d:sxsort3d [2018/02/23 18:15]
moriya
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   ; mask : 3D mask: File path of the global 3D mask for clustering. (default none)   ; mask : 3D mask: File path of the global 3D mask for clustering. (default none)
  
-  ; focus : Binary Focus 3D mask: Binary 3D mask used for focused clustering. (default none) +  ; %%--%%focus : Binary Focus 3D mask: Binary 3D mask used for focused clustering. (default none) 
-  ; radius : Particle radius [Pixels]: Used as outer radius for rotational correlation.  Must be smaller than half the box size. (default -1) +  ; %%--%%radius : Particle radius [Pixels]: Used as outer radius for rotational correlation.  Must be smaller than half the box size. (default -1) 
-  ; delta : Angular step for projections [Degrees]: Angular step of reference projections. (default '2') +  ; %%--%%delta : Angular step for projections [Degrees]: Angular step of reference projections. (default '2') 
-  ; CTF : Use CTF: Do a full CTF correction during the alignment. (default False) +  ; %%--%%CTF : Use CTF: Do a full CTF correction during the alignment. (default False) 
-  ; sym : Point-group symmetry: Point-group symmetry of the target structure. (default c1) +  ; %%--%%sym : Point-group symmetry: Point-group symmetry of the target structure. (default c1) 
-  ; number_of_images_per_group : Images per group: Critical value defined by user. It suggests program the number of groups. (default 1000) +  ; %%--%%number_of_images_per_group : Images per group: Critical value defined by user. It suggests program the number of groups. (default 1000) 
-  ; nxinit : Initial image size for sorting: Initial image size for sorting. (default 64) +  ; %%--%%nxinit : Initial image size for sorting: Initial image size for sorting. (default 64) 
-  ; smallest_group : Smallest group size: Minimum members for identified group. (default 500)  +  ; %%--%%smallest_group : Smallest group size: Minimum members for identified group. (default 500)  
-  ; chunk0 : Chunk file name for 1st halfset: Name of chunk file containing particle IDs of 1st halfset (chunk0) for computing margin of error. (default none) +  ; %%--%%chunk0 : Chunk file name for 1st halfset: Name of chunk file containing particle IDs of 1st halfset (chunk0) for computing margin of error. (default none) 
-  ; chunk1 : Chunk file name for 2nd halfset: Name of chunk file containing particle IDs of 2nd halfset (chunk1) for computing margin of error. (default none)+  ; %%--%%chunk1 : Chunk file name for 2nd halfset: Name of chunk file containing particle IDs of 2nd halfset (chunk1) for computing margin of error. (default none)
  
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 === Advanced Parameters === === Advanced Parameters ===
-  ; ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1) +  ; %%--%%ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1) 
-  ; maxit : Maximum iterations: Maximum number of iteration. (default 25) +  ; %%--%%maxit : Maximum iterations: Maximum number of iteration. (default 25) 
-  ; rs : Step between rings in rotational correlation: Must be bigger than 0. (default 1) +  ; %%--%%rs : Step between rings in rotational correlation: Must be bigger than 0. (default 1) 
-  ; xr : X search range [Pixels]: The translational search range in the x direction will take place in -xr to +xr range. (default '1') +  ; %%--%%xr : X search range [Pixels]: The translational search range in the x direction will take place in -xr to +xr range. (default '1') 
-  ; yr : Y search range [Pixels]: The translational search range in the y direction will take place in -yr to +yr range.. If omitted, it will be set as xr. (default '-1') +  ; %%--%%yr : Y search range [Pixels]: The translational search range in the y direction will take place in -yr to +yr range.. If omitted, it will be set as xr. (default '-1') 
-  ; ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default '0.25') +  ; %%--%%ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default '0.25') 
-  ; an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default '-1') +  ; %%--%%an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default '-1') 
-  ; center : Centering method: 0 - if you do not want the volume to be centered, 1 - center the volume using the center of gravity. (default 0) +  ; %%--%%center : Centering method: 0 - if you do not want the volume to be centered, 1 - center the volume using the center of gravity. (default 0) 
-  ; nassign : Number of reassignment iterations: Performed for each angular step. (default 1) +  ; %%--%%nassign : Number of reassignment iterations: Performed for each angular step. (default 1) 
-  ; nrefine : Number of alignment iterations: Performed for each angular step. (default 0) +  ; %%--%%nrefine : Number of alignment iterations: Performed for each angular step. (default 0) 
-  ; stoprnct : Assignment convergence threshold [%]: Used to asses convergence of the run. It is the minimum percentage of assignment change required to stop the run.  (default 3.0) +  ; %%--%%stoprnct : Assignment convergence threshold [%]: Used to asses convergence of the run. It is the minimum percentage of assignment change required to stop the run.  (default 3.0) 
-  ; function : Reference preparation function: Specify name of function used to prepare the reference volume. (default do_volume_mrk05) +  ; %%--%%function : Reference preparation function: Specify name of function used to prepare the reference volume. (default do_volume_mrk05) 
-  ; independent : Number of independent runs: Number of independent equal-Kmeans. (default 3) +  ; %%--%%independent : Number of independent runs: Number of independent equal-Kmeans. (default 3) 
-  ; low_pass_filter : Low-pass filter frequency [1/Pixels]: Low-pass filter used for the 3D sorting on the original image size. Specify with absolute frequency. (default -1.0) +  ; %%--%%low_pass_filter : Low-pass filter frequency [1/Pixels]: Low-pass filter used for the 3D sorting on the original image size. Specify with absolute frequency. (default -1.0) 
-  ; unaccounted : Reconstruct unaccounted images: Reconstruct unaccounted images. (default False) +  ; %%--%%unaccounted : Reconstruct unaccounted images: Reconstruct unaccounted images. (default False) 
-  ; seed : Random seed: Seed used for the initial random assignment for EQ Kmeans. The program generates a random integer by default. (default -1) +  ; %%--%%seed : Random seed: Seed used for the initial random assignment for EQ Kmeans. The program generates a random integer by default. (default -1) 
-  ; sausage : Use sausage filter: A way of filtering volume. (default False) +  ; %%--%%sausage : Use sausage filter: A way of filtering volume. (default False) 
-  ; PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum used for EM density map power spectrum correction. Typically, compute 1D power spectrum from PDB file. (default none) +  ; %%--%%PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum used for EM density map power spectrum correction. Typically, compute 1D power spectrum from PDB file. (default none) 
-  ; protein_shape : Protein Shape: It defines protein preferred orientation angles. "g" is for globular proteins and "f" is for filament proteins. (default 'g') +  ; %%--%%protein_shape : Protein Shape: It defines protein preferred orientation angles. "g" is for globular proteins and "f" is for filament proteins. (default 'g') 
-  ; upscale : Power spectrum adjustment strength: This parameters adjusts how strongly the power spectrum of the volume should be modified to match the reference. A value of 1 brings the volume's power spectrum completely to the reference, while a value of 0 means no modification. (default 0.5) +  ; %%--%%upscale : Power spectrum adjustment strength: This parameters adjusts how strongly the power spectrum of the volume should be modified to match the reference. A value of 1 brings the volume's power spectrum completely to the reference, while a value of 0 means no modification. (default 0.5) 
-  ; wn : Target image size [Pixels]: Specify optimal window size for data processing. If different than 0, then the images will be rescaled to fit this size. (default 0) +  ; %%--%%wn : Target image size [Pixels]: Specify optimal window size for data processing. If different than 0, then the images will be rescaled to fit this size. (default 0) 
-  ; interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default '4nn')+  ; %%--%%interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default '4nn')
  
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 ==== See also ==== ==== See also ====
-[[pipeline:utilities:sxheader|sxheader]], [[[pipeline:sort3d:sx3dvariability|sx3dvariability]], [[pipeline:sort3d:sxsort3d_depth|sxsort3d_depth]] and [[pipeline:sort3d:sxrsort3d|sxrsort3d]]+[[pipeline:meridien:sxmeridien|sxmeridien]], [[pipeline:utilities:sxheader|sxheader]], [[[pipeline:sort3d:sx3dvariability|sx3dvariability]], [[pipeline:sort3d:sxrsort3d|sxrsort3d]], and [[pipeline:sort3d:sxsort3d_depth|sxsort3d_depth]].
  
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pipeline/sort3d/sxsort3d.txt · Last modified: 2019/04/02 10:49 by lusnig

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