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

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

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.)

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.

Numbers of particles vs. resolutions of four groups of classes

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*')

--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)

bfactor.png

Plot of Number of particles versus resolution

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.

Tapu Shaikh & Sabrina Pospich

Category 1:: APPLICATIONS

sphire/bin/sp_bfactor_plot.py

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

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