pipeline:utilities:sxpipe_angular_distribution

This version (2019/04/02 10:54) is a draft.
Approvals: 0/1

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


Usage in command line

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


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.

Do angular distribution to generate a chimera .bild file based on the projection parameters stored in params_file.

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.

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.

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. However, using small delta values might crash chimera session depending on the computers available memory.

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

sp_pipe.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 to be applied to 3D reconstruction (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/sp_pipe.py


Alpha:: Under development.


There are no known bugs so far.


  • pipeline/utilities/sxpipe_angular_distribution.txt
  • Last modified: 2019/04/02 10:54
  • by lusnig