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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] (current) lusnig [See also] |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxpipe | + | ===== sp_pipe |
Angular Distribution: | Angular Distribution: | ||
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Usage in command line | Usage in command line | ||
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===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxpipe | + | sp_pipe |
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. | ||
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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. | ||
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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. | ||
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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. | ||
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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. | ||
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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 | + | ; %%--%%symmetry : Point-group symmetry: Symmetry |
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==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxpipe.py | + | sparx/bin/sp_pipe.py |
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==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
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