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

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)

--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)

This program overwrites existing output_folder/prefix combinations.

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

Markus Stabrin

Category 1:: APPLICATIONS

sparx/bin/sxpipe.py

sxmeridien.

Alpha:: Under development.

There are no known bugs so far.