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pipeline:window:sxwindow [2020/09/23 15:20]
aali [Files]
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 '.txt'. Alternatively, the file name of a single micrograph can be specified for Single Micrograph Mode. (default none)   ; %%--%%selection_list : Micrograph selection file: Specify a name of micrograph selection list text file for Selected Micrographs Mode. The file extension must be '.txt'. Alternatively, the file name of a single micrograph can be specified for Single Micrograph Mode. (default none)
-  ; %%--%%coordinates_format : Coordinate file format: Allowed values are 'sphire', 'eman1', 'eman2', 'cryolo'','cryolo_helical_segmented' or 'spider'. The sphire, eman2, and spider formats use the particle center as coordinates. The eman1 format uses the lower left corner of the box as coordinates. (default cryolo)+  ; %%--%%coordinates_format : Coordinate file format: Allowed values are 'sphire', 'eman1', 'eman2', 'cryolo','cryolo_helical_segmented' or 'spider'. The sphire, eman2, and spider formats use the particle center as coordinates. The eman1 format uses the lower left corner of the box as coordinates. (default cryolo|||eman1|||eman2|||cryolo_helical_segmented)
   ; %%--%%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 when the CTER CTF File is not specified by the CTF paramters source argument. (default False) +  ; %%--%%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 when the CTER CTF File is not specified by the CTF paramters source argument. (default False) 
-  ; %%--%%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 when the CTER CTF File is not specified by the CTF paramters source argument. (default 360.0)+  ; %%--%%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 has no effect when the CTER CTF File is not specified by the CTF paramters source argument. (default 360.0)
   ; %%--%%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)   ; %%--%%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 it uses one third of the box size. (default -1)+  ; %%--%%filament_width : Filament width [Pixels] : Filament width for the creation of the rectangular mask. If -1 is selected, no mask will be applied. (default -1)::-1;Main
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 ===== Output ===== ===== Output =====
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 ==== See also ==== ==== See also ====
-[[pipeline:cter:sxcter|sp_cter]] and [[pipeline:window:e2boxer_old|e2boxer_old]]+[[pipeline:cter:sp_cter|sp_cter]] and [[pipeline:window:e2boxer_old|e2boxer_old]]
  
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pipeline/window/sxwindow.txt · Last modified: 2022/05/25 13:47 by shaikh