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sp_bfactor_plot
This version (2020/07/23 10:19) is a draft.
Approvals: 0/1

sp_bfactor_plot

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


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


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.)

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


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*')


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)


Output

bfactor.png
Plot of Number of particles versus resolution


Description


Method


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.

Developer Notes


Author / Maintainer

Tapu Shaikh & Sabrina Pospich


Keywords

Category 1:: APPLICATIONS


Files

sphire/bin/sp_bfactor_plot.py


See also


Maturity

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


Bugs

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


sp_bfactor_plot.txt ยท Last modified: 2020/07/23 10:19 by shaikh