pipeline:utilities:sxpipe_angular_distribution

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pipeline:utilities:sxpipe_angular_distribution [2018/08/22 11:30]
fmerino created
pipeline:utilities:sxpipe_angular_distribution [2019/04/02 10:54]
lusnig [See also]
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxpipe ​angular_distribution =====+===== sp_pipe ​angular_distribution =====
 Angular Distribution:​ Generate a chimera .bild file for the visual representation of the resulting projection parameters. Angular Distribution:​ Generate a chimera .bild file for the visual representation of the resulting projection parameters.
  
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 Usage in command line Usage in command line
  
-  ​sxpipe.py  angular_distribution ​ params_file ​ output_folder ​ --prefix=None --method=S --pixel_size=1.0 --delta=3.75 --symmetry=c1 --box_size=256 --particle_radius=120 --dpi=72+  ​sp_pipe.py  angular_distribution ​ params_file ​ output_folder ​ --prefix=None --method=S --pixel_size=1.0 --delta=3.75 --symmetry=c1 --box_size=256 --particle_radius=120 --dpi=72
  
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 ===== Typical usage ===== ===== Typical usage =====
  
-sxpipe ​angular distribution does not support MPI. +sp_pipe ​angular distribution does not support MPI. 
  
 Bild files created with small delta values might crash chimera session depending on the computer available memory. Bild files created with small delta values might crash chimera session depending on the computer available memory.
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 Do angular distribution to generate a chimera .bild file based on the projection parameters stored in params_file. Do angular distribution to generate a chimera .bild file based on the projection parameters stored in params_file.
  
-  ​sxpipe.py angular_distribution ​ params_file output_folder+  ​sp_pipe.py angular_distribution ​ params_file output_folder
  
 By default, the resulting .bild file has the same name as the params_file. Use the --prefix option to change the name. By default, the resulting .bild file has the same name as the params_file. Use the --prefix option to change the name.
  
-  ​sxpipe.py angular_distribution ​ params_file output_folder --prefix=my_name+  ​sp_pipe.py angular_distribution ​ params_file output_folder --prefix=my_name
  
 Adjust the pixel_size, box_size and particle_radius values if the .bild file will be opened together with the structure in chimera. Adjust the pixel_size, box_size and particle_radius values if the .bild file will be opened together with the structure in chimera.
  
-  ​sxpipe.py angular_distribution ​ params_file output_folder --pixel_size=1.14 --box_size=120 --particle_radius=50+  ​sp_pipe.py angular_distribution ​ params_file output_folder --pixel_size=1.14 --box_size=120 --particle_radius=50
  
 To adjust the number of bins used in the 3D histogram, use the --delta option. To adjust the number of bins used in the 3D histogram, use the --delta option.
 However, using small delta values might crash chimera session depending on the computers available memory. However, using small delta values might crash chimera session depending on the computers available memory.
  
-  ​sxpipe.py angular_distribution ​ params_file output_folder --delta=1.875+  ​sp_pipe.py angular_distribution ​ params_file output_folder --delta=1.875
  
 Next to the bild file, a .png legends file will be created, that translates the bin color into real particle numbers. Next to the bild file, a .png legends file will be created, that translates the bin color into real particle numbers.
 With the --dpi option, one can adjust the quality of the plot. With the --dpi option, one can adjust the quality of the plot.
  
-  ​sxpipe.py angular_distribution ​ params_file output_folder --dpi=300+  ​sp_pipe.py angular_distribution ​ params_file output_folder --dpi=300
  
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  ; output_folder : Output directory: Output folder name (default required string)  ; output_folder : Output directory: Output folder name (default required string)
  ; %%--%%prefix : File prefix : Prefix for the output files - None uses the same name as the params file - Existing files will be overridden (default none)  ; %%--%%prefix : File prefix : Prefix for the output files - None uses the same name as the params file - Existing files will be overridden (default none)
- ; %%--%%symmetry : Point-group symmetry: Symmetry ​- sym_full creates full sphere distribution,​ e.g. c1_full, icos_full ​(default c1)+ ; %%--%%symmetry : Point-group symmetry: Symmetry ​to be applied to 3D reconstruction ​(default c1)
  
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 ==== Files ==== ==== Files ====
-sparx/bin/sxpipe.py+sparx/bin/sp_pipe.py
  
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 ==== See also ==== ==== See also ====
-[[pipeline:​meridien:​sxmeridien|sxmeridien]].+[[pipeline:​meridien:​sxmeridien|sp_meridien]].
  
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  • pipeline/utilities/sxpipe_angular_distribution.txt
  • Last modified: 2019/04/02 10:54
  • by lusnig