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pipeline:sort3d:sx3dvariability [2018/05/14 16:19] 127.0.0.1 external edit |
pipeline:sort3d:sx3dvariability [2018/08/22 10:31] fmerino |
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Usage in command line | Usage in command line | ||
- | sx3dvariability.py | + | sx3dvariability.py |
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; %%--%%output_dir : Output directory: Specify path to the output directory of 3D Variability. By default, the program uses the current directory. However, GUI requires the path other than the current directory. (default required string) | ; %%--%%output_dir : Output directory: Specify path to the output directory of 3D Variability. By default, the program uses the current directory. However, GUI requires the path other than the current directory. (default required string) | ||
; %%--%%var3D : Output 3D variability: | ; %%--%%var3D : Output 3D variability: | ||
- | ; %%--%%ave3D : Output 3D average: Specify a file name to indicate if the program should write the reconstructed 3D average map to the disk. The 3D volume | + | ; %%--%%ave3D : Output 3D average: Specify a file name to indicate if the program should write the reconstructed 3D average map to the disk. The 3D map will be reconstructed from projections averaged within respective angular neighbourhood. It should be used to assess the resolvability and possible artifacts of the variability map. (default none) |
- | ; %%--%%img_per_grp : Number of projections: | + | ; %%--%%img_per_grp : Number of projections: |
; %%--%%sym : Point-group symmetry: If the structure has symmetry higher than c1, the command requires symmetrization of the dataset, using %%--%%symmetrize option, before computing 3D variability. (default c1) | ; %%--%%sym : Point-group symmetry: If the structure has symmetry higher than c1, the command requires symmetrization of the dataset, using %%--%%symmetrize option, before computing 3D variability. (default c1) | ||
- | ; %%--%%CTF : Use CTF: If set to true, the a CTF correction will be applied using the parameters found in the image headers. (default False value reversed in GUI) | + | ; %%--%%CTF : Use CTF correction: If set to true, CTF correction will be applied using the parameters found in the image headers. (default False value reversed in GUI) |
- | ; %%--%%fl : Low-pass filter frequency [1/Pixel]: Stop-band frequency of the low-pass filter to be applied to the images prior to variability calculation. Specify it in absolute frequency (%%>%% 0.0 and %%<=%% 0.5). By default, no filtering. (default 0.0) | + | ; %%--%%fl : Low-pass filter frequency [1/Pixel]: Stop-band frequency of the low-pass filter to be applied to the images prior to variability calculation |
- | ; %%--%%aa : Low-pass filter fall-off [1/Pixel]: Fall-off width of the low-pass filter to be applied to the images prior to variability calculation. Specify it in absolute frequency (%%>%% 0.0 and %%<=%% 0.5). 0.01 works in most of cases. Effective only with %%--%%fl %%>%% 0.0 and %%--%%aa %%>%% 0.0 has to be specified. (default 0.0) | + | ; %%--%%aa : Low-pass filter fall-off [1/Pixel]: Fall-off width of the low-pass filter to be applied to the images prior to variability calculation |
; %%--%%symmetrize : Symmetrise input stack: Prepare input stack for handling symmetry. Please skip this preparation step if the structure is asymmetrical (i.e. c1), since it is required only when the structure has internal symmetry. Notice this step can be run with only one CPU and there is no MPI version for it. (default False) | ; %%--%%symmetrize : Symmetrise input stack: Prepare input stack for handling symmetry. Please skip this preparation step if the structure is asymmetrical (i.e. c1), since it is required only when the structure has internal symmetry. Notice this step can be run with only one CPU and there is no MPI version for it. (default False) | ||
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; %%--%%no_norm : Apply normalization: | ; %%--%%no_norm : Apply normalization: | ||
; %%--%%npad : Image padding factor: The number of time to pad the original images. The images will be padded to achieve the original size times this option. (default 2) | ; %%--%%npad : Image padding factor: The number of time to pad the original images. The images will be padded to achieve the original size times this option. (default 2) | ||
- | ; %%--%%decimate : Image decimate factor: Reduce images by this factor and change the pixel size. Specify a value large than 1.0 to expand images, and less than 1.0 to shrink them. By default, it does not change size of images. (default 1.0) | + | ; %%--%%decimate : Image decimate factor: Reduce images by this factor and change the pixel size. Specify a non-zero positive float value smaller |
- | ; %%--%%window : User smaller window | + | ; %%--%%window : Target image size [Pixels]: Window (or clip) images using the specified size without changing pixel size. It is relative to the orignal window size. The target window size cannot be larger than the orignal image size. By default, use the original particle image size. (default 0) |
; %%--%%nvec : Number of eigenvectors: | ; %%--%%nvec : Number of eigenvectors: | ||
; %%--%%VERBOSE : Verbose: Print long output which is useful for debugging. (default False) | ; %%--%%VERBOSE : Verbose: Print long output which is useful for debugging. (default False) | ||
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