sp_bfactor_plot []

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===== sp_bfactor_plot =====
Plot B-factor : Plots number of particles versus resolution.

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===== Usage =====

Usage in command line:

  sp_bfactor_plot.py search_directory output_directory --mode=mode --groups=groups --flo=flo --display=display_exe --verbosity=verbosity --sharpendir=sharpendir --selectpattern=selectpattern --resfile=resfile --apix=apix
  
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===== Typical usage =====
The purpose of sp_bfactor_plot.py is to: 
  : plot the number of particles versus resolution

\\ __1. Standard usage: create separate stacks for each class__:

    sp_bfactor_plot.py search_directory output_directory --mode=2d_or_3d --groups=number_of_groups

If number of groups is not specified, all classes will have the same color. If groups of classes are found, then they can be colored differently. 

\\ __2. 2D: Gets number of particles from params_avg* files and resolution from beautifier directories__:

  sp_bfactor_plot.py search_directory output_directory --mode=2d --groups=number_of_groups

Specifically, program will look for a beautifier file called 'FH_list.txt' to get the resolution, and parameter files called 'params_avg*' to get the number of particles. If your files have other names, see the advanced parameters below. (The development version of the beautifier stores all information in 'FH_list.txt', and doesn't use an unrealistically optimistic resolution estimate.)
[{{ :bfactor2d.png?600 |Numbers of particles vs. resolutions of two groups of classes}}]
\\ __3. 3D: Gets number of particles from Meridien directories and resolution from PostRefiner directories__:

  sp_bfactor_plot.py search_directory output_directory --mode=3d --groups=number_of_groups

Program will look for a PostRefiner file called 'log.txt' to get the resolutions, and a parameter file called 'final_params*' to get the number of particles. If your files have other names, see the advanced parameters below. Program will also attempt to fit points.
[{{ ::bfactor3d.png?600 |Numbers of particles vs. resolutions of four groups of classes}}]
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===== Input =====
=== Main Parameters ===
  ; search_directory : Directory where input files fill be searched
  ; output_directory : Directory where outputs will be written. (default required string)
  ; %%--%%groups : Number of groups to plot. (default 1)
  ; %%--%%flo : Lowest resolution on plot, Angstroms. (default 7)
  ; %%--%%apix : pixel size (needed in 2d mode for old-style 3-column 'FH_list.txt' files). (default 'final_params*' or 'params_avg*')
  
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=== Advanced Parameters ===
  ; %%--%%sharpendir : Subdirectory to look for PostRefiner resolution file. (default None)
  ; %%--%%selectpattern : Alignment-parameter file template, enclosed in quotes. (default None)
  ; %%--%%resfile : Resolution file. (default 'FH_list.txt' for 2d or 'log.txt' for 3d)

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===== Output =====
  ; bfactor.png : Plot of Number of particles versus resolution

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===== Description =====

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==== Method ====

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==== Reference ====
Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.
Rosenthal PB, Henderson R. J Mol Biol. 2003 Oct 31;333(4):721-45. doi: 10.1016/j.jmb.2003.07.013.
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==== Developer Notes ====

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==== Author / Maintainer ====
Tapu Shaikh & Sabrina Pospich

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

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==== Files ====
sphire/bin/sp_bfactor_plot.py

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==== See also ====

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==== Maturity ====
Beta:: Under evaluation and testing. Please let us know if there are any bugs.

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==== Bugs ====
Automatic display of plots does not always work (file system not refreshed yet?).

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