~~NOTOC~~

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

\\
===== Usage =====

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

\\
===== Typical usage =====

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

\\
===== Input =====
=== 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)

\\
===== Output =====
=== 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. ||

\\
===== Description =====
This program overwrites existing output_folder/prefix combinations.

\\
==== Method ====

\\
==== Reference ====

\\
==== Developer Notes ====
=== 2018/08/09 Markus Stabrin ===
    * High symmetries take about 1-2 minutes.
    * Low delta values might crash the chimera session.

\\
==== Author / Maintainer ====
Markus Stabrin


\\
==== Keywords ====
Category 1:: APPLICATIONS

\\
==== Files ====
sparx/bin/sp_pipe.py

\\
==== See also ====
[[pipeline:meridien:sxmeridien|sp_meridien]].

\\
==== Maturity ====
Alpha:: Under development.

\\
==== Bugs ====
There are no known bugs so far.

\\