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

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)

--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/sp_pipe.py

sp_meridien.

Alpha:: Under development.

There are no known bugs so far.