pipeline:utilities:sxpipe_angular_distribution

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Angular Distribution: Generate a chimera .bild file for the visual representation of the resulting projection parameters.


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


sxpipe angular distribution does not support MPI.

Bild files created with small delta values might crash chimera session depending on the computer available memory.

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

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

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

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.

sxpipe.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. With the –dpi option, one can adjust the quality of the plot.

sxpipe.py angular_distribution  params_file output_folder --dpi=300


Main Parameters

params_file
Projection parameters
File containing the 3D projection parameters (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)
--symmetry
Point-group symmetry: Symmetry - sym_full creates full sphere distribution, e.g. c1_full, icos_full (default c1)


Advanced Parameters

--pixel_size
Pixel size [A]
Pixel size of the project (default 1.0)
--delta
Angular sampling step [Degrees]
Angular step size in degree - Low deltas combined with low symmetry might crash chimera session (default 3.75)
--box_size
Particle box size [Pixels]
Box size (default 256)
--particle_radius
Particle radius [Pixels]
Particle radius (default 120)
--method
Distribution method
Method used to create the reference angles (S or P) (default S)
--dpi
Plot DPI
Dpi for the legend plot (default 72)


List of output Files

File Name Discription
output_directory/prefix.bild 3D histogram that can be opened in UCSF chimera.
output_directory/prefix.png 2D histogram that correlates the bin color with the real particle number.
output_directory/prefix.txt Text file containing the 2D histogram data points.


This program overwrites existing output_folder/prefix combinations.




2018/08/09 Markus Stabrin

  • High symmetries take about 1-2 minutes.
  • Low delta values might crash the chimera session.


Markus Stabrin


Category 1:: APPLICATIONS


sparx/bin/sxpipe.py


Alpha:: Under development.


There are no known bugs so far.


  • pipeline/utilities/sxpipe_angular_distribution.1534930236.txt.gz
  • Last modified: 2018/08/22 11:30
  • by fmerino