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pipeline:window:sxwindow [2019/04/02 09:19] lusnig |
pipeline:window:sxwindow [2022/05/25 13:47] shaikh |
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; %%--%%selection_list : Micrograph selection file: Specify a name of micrograph selection list text file for Selected Micrographs Mode. The file extension must be ' | ; %%--%%selection_list : Micrograph selection file: Specify a name of micrograph selection list text file for Selected Micrographs Mode. The file extension must be ' | ||
- | ; %%--%%coordinates_format : Coordinate file format: Allowed values are ' | + | ; %%--%%coordinates_format : Coordinate file format: Allowed values are ' |
; %%--%%box_size : Particle box size [Pixels]: The x and y dimensions of square area to be windowed. The box size after resampling is assumed when resample_ratio < 1.0. (default 256) | ; %%--%%box_size : Particle box size [Pixels]: The x and y dimensions of square area to be windowed. The box size after resampling is assumed when resample_ratio < 1.0. (default 256) | ||
; %%--%%skip_invert : Invert image contrast: Indicate if image contrast should be inverted or not. Do not invert for negative staining data. By default, the image contrast will be inverted for cryo data. (default False question reversed in GUI) | ; %%--%%skip_invert : Invert image contrast: Indicate if image contrast should be inverted or not. Do not invert for negative staining data. By default, the image contrast will be inverted for cryo data. (default False question reversed in GUI) | ||
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=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; %%--%%limit_ctf : Use CTF limit filter: Frequencies where CTF oscillations cannot be properly modeled with the resampled pixel size will be discarded in the images with the appropriate low-pass filter. This has no effects | + | ; %%--%%limit_ctf : Use CTF limit filter: Frequencies where CTF oscillations cannot be properly modeled with the resampled pixel size will be discarded in the images with the appropriate low-pass filter. This flag has no effect |
- | ; %%--%%astigmatism_error : Astigmatism error limit [Degrees]: Set astigmatism to zero for all micrographs where the angular error computed by sp_cter is larger than the desired value. This has no effects | + | ; %%--%%astigmatism_error : Astigmatism error limit [Degrees]: Set astigmatism to zero for all micrographs where the angular error computed by sp_cter is larger than the desired value. This parameter |
; %%--%%resample_ratio : Image size reduction factor (<1): Use a value between 0.0 and 1.0 (excluding 0.0). The new pixel size will be automatically recalculated and stored in CTF paramers when resample_ratio < 1.0 is used. (default 1.0) | ; %%--%%resample_ratio : Image size reduction factor (<1): Use a value between 0.0 and 1.0 (excluding 0.0). The new pixel size will be automatically recalculated and stored in CTF paramers when resample_ratio < 1.0 is used. (default 1.0) | ||
; %%--%%check_consistency : Check consistency of inputs: Create a text file containing the list of inconsistent Micrograph ID entries (i.e. inconsist_mic_list_file.txt). (default False) | ; %%--%%check_consistency : Check consistency of inputs: Create a text file containing the list of inconsistent Micrograph ID entries (i.e. inconsist_mic_list_file.txt). (default False) | ||
- | ; %%--%%filament_width : Filament width : Filament width for the creation of the rectangular mask. When -1 is selected | + | ; %%--%%filament_width : Filament width [Pixels] |
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===== Output ===== | ===== Output ===== | ||
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==== Files ==== | ==== Files ==== | ||
- | sparx/ | + | sphire/ |
\\ | \\ |