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pipeline:window:sxwindow [2018/06/20 13:12]
127.0.0.1 external edit 		pipeline:window:sxwindow [2018/08/22 11:42]
fmerino
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 \\ __1. All Micrographs Mode - Process all micrographs in a directory:__ \\ __1. All Micrographs Mode - Process all micrographs in a directory:__
-\\ Specify path pattern of input micrographs and coordinates files with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between a associated pair of input micrograph and coordinates file. bdb files can not be selected as input micrographs. Next, specify the source of CTF paramters. For cryo data, this should be the file produced by sxcter and normally called partres.txt. For negative staining data, it should be the pixel size [A/Pixels] of input micrographs. Finally, specify output directory where all outputs should be saved. In this mode, all micrographs matching the path pattern will be processed.+\\ Specify path pattern of input micrographs and coordinates files with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between a associated pair of input micrograph and coordinates file. bdb files cannot be selected as input micrographs. Next, specify the source of CTF paramters. For cryo data, this should be the file produced by sxcter and normally called partres.txt. For negative staining data, it should be the pixel size [A/Pixels] of input micrographs. Finally, specify output directory where all outputs should be saved. In this mode, all micrographs matching the path pattern will be processed.
   mpirun  -np  32  sxwindow.py  './mic*.hdf'  'info/mic*_info.json'  outdir_cter/partres/partres.txt  particles  --coordinates_format=eman2  --box_size=64   mpirun  -np  32  sxwindow.py  './mic*.hdf'  'info/mic*_info.json'  outdir_cter/partres/partres.txt  particles  --coordinates_format=eman2  --box_size=64
  
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 ===== Input ===== ===== Input =====
 === Main Parameters === === Main Parameters ===
-  ; input_micrograph_pattern : Input micrograph path pattern: Specify path pattern of input micrographs with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between the associated pair of input micrograph and coordinates file. bdb files can not be selected as input micrographs. (default required string) +  ; input_micrograph_pattern : Input micrograph path pattern: Specify path pattern of input micrographs with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between the associated pair of input micrograph and coordinates file. bdb files cannot be selected as input micrographs. (default required string) 
-  ; input_coordinates_pattern : Input coordinates path pattern: Specify path pattern of input coordinates files with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between the associated pair of input micrograph and coordinates file. (default required string)+  ; input_coordinates_pattern : Input coordinates path pattern: Specify path pattern of input coordinates files with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between the associated pair of input micrograph and coordinates file. (default required string)
   ; input_ctf_params_source : CTF parameters source: Specify the file produced by sxcter and normally called partres.txt for cryo data. For negative staining data, enter pixel size [A/Pixels]. (default required string)   ; input_ctf_params_source : CTF parameters source: Specify the file produced by sxcter and normally called partres.txt for cryo data. For negative staining data, enter pixel size [A/Pixels]. (default required string)
-  ; output_directory : Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)+  ; output_directory : Output directory: The results will be written here. It cannot be an existing one. (default required string)
  
   ; %%--%%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)
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 === Advanced Parameters === === Advanced Parameters ===
-  ; %%--%%limit_ctf : Use CTF limit filter: Frequencies where CTF oscillations can not 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 has no effects 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 sxcter 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 sxcter 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)
   ; %%--%%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)
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 ===== Output ===== ===== Output =====
-Inside the output directory, the program will write a local BDB stack image for each micrograph. The files are named micrograph name with "_ptcls" suffix. For example, ''particles/EMAN2DB/mic0_ptcls.bdb'' or ''bdb:particles#mic0_ptcls'' +Inside the output directory, the program will write a local bdb stack image for each micrograph. The files are named micrograph name with "_ptcls" suffix. For example, ''particles/EMAN2DB/mic0_ptcls.bdb'' or ''bdb:particles#mic0_ptcls'' 
  
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pipeline/window/sxwindow.txt · Last modified: 2022/05/25 13:47 by shaikh

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