Segrefine3dcyclexplore¶

Program to interactively explore refinement cycle statistics

Input: refinement.db file

Output: Interactive screenshot

Parameters¶

Parameter	Example (default)	Description
refinement.db file	refinement.db	Requires refinement.db from segmentrefine3d to extract refinment parameters.
Batch mode	False	Batch mode for plot. Otherwise interactive.

Sample parameter file¶

You may run the program in the command line by providing the parameters via a text file:

segrefine3dcyclexplore --f parameterfile.txt

Where the format of the parameters is:

refinement.db file                       = refinement.db
Batch mode                               = False

Additional parameters (intermediate level)¶

Parameter	Example (default)	Description
Diagnostic plot prefix	diagnostic_plot.pdf	Output name for diagnostic plots of iterative structure refinement (completion to ‘prefix_XXX.ext’): accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff).
Criterion	mean_helical_ccc	Refinement criteria of refinement to be plotted: ‘fsc_0143’: FSC cutoff 0.143 - Fourier shell correlation at 0.143 cutoff Rosenthal/Henderson criterion in Angstrom.; ‘fsc_05’: FSC cutoff 0.5 - Fourier shell correlation at 0.5 cutoff criterion in Angstrom.; ‘xshift_error’: Shift error perpendicular to helix in Angstrom - derived from RMS deviation of forward difference between successive segments.; ‘inplane_error’: In-plane rotation error perpendicular to helix in degrees - derived from RMS deviation of forward difference between successive segments.; ‘outofplane_error’: Out-of-plane tilt error to helix in degrees - derived from RMS deviation of forward difference between successive segments.; ‘mean_peak’: Mean peak - of projection matching between experimental images and reprojections.; ‘amp_corr_quarter_nyquist’: Average amplitude correlation up to quarter Nyquist cutoff - between experimental and simulated power spectrum.; ‘amp_corr_half_nyquist’: Average amplitude correlation up to half Nyquist cutoff - between experimental and simulated power spectrum.; ‘amp_corr_3quarter_nyquist’: Average amplitude correlation up to three quarter Nyquist cutoff - between experimental and simulated power spectrum.; ‘amp_correlation’: Average amplitude correlation - between experimental and simulated power spectrum.; ‘helical_ccc_error’: Helical CCC error - Mean of standard deviations of CCC values from all asymmetric unit views with their corresponding reprojections.; ‘mean_helical_ccc’: Mean helical CCC - Mean of CCC values from all asymmetric unit views with their corresponding reprojections.; ‘out_of_plane_dev’: Out of plane tilt deviation - Standard deviationof out-of-plane tilt angles ; ‘variance’: Variance - of 3D reconstruction.; ‘asym_unit_count’: Asymmetric unit count - Number of asymmetric units included in 3D reconstruction.; ‘avg_azimuth_sampling’: Azimuthal sampling average - Average of sampling of phi angles around helical axis; ‘dev_azimuth_sampling’: Azimuthal sampling standard deviation - Standard deviation of sampling of phi angles around helical axis; ‘excluded_out_of_plane_tilt_count’: Excluded out-of-plane segment count - based on out-of-plane tilt angle criterion; ‘excluded_inplane_count’: Excluded inplane segment count - based on in-plane rotation angle criterion; ‘total_excluded_count’: Excluded segment count - based on applied refinement criteria;

Sample parameter file (intermediate level)¶

You may run the program in the command line by providing the parameters via a text file:

segrefine3dcyclexplore --f parameterfile.txt

Where the format of the parameters is:

refinement.db file                       = refinement.db
Batch mode                               = False
Diagnostic plot prefix                   = diagnostic_plot.pdf
Criterion                                = mean_helical_ccc

Additional parameters (expert level)¶

Parameter	Example (default)	Description

Sample parameter file (expert level)¶

You may run the program in the command line by providing the parameters via a text file:

segrefine3dcyclexplore --f parameterfile.txt

Where the format of the parameters is:

refinement.db file                       = refinement.db
Batch mode                               = False
Diagnostic plot prefix                   = diagnostic_plot.pdf
Criterion                                = mean_helical_ccc

Command line options¶

When invoking segrefine3dcyclexplore, you may specify any of these options:

usage: segrefine3dcyclexplore [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--batch_mode]
                              [input_output [input_output ...]]

Program to interactively explore refinement cycle statistics

positional arguments:
  input_output          Input and output files

optional arguments:
  -h, --help            show this help message and exit
  --g, --GUI            GUI option: read input parameters from GUI
  --p, --promptuser     Prompt user option: read input parameters from prompt
  --f FILENAME, --parameterfile FILENAME
                        File option: read input parameters from FILENAME
  --c, --cmd            Command line parameter option: read only boolean input parameters from command line and all other parameters will be assigned
                        from other sources
  --l LOGFILENAME, --logfile LOGFILENAME
                        Output logfile name as specified
  --d DIRECTORY_NAME, --directory DIRECTORY_NAME
                        Output directory name as specified
  --version             show program's version number and exit
  --batch_mode, --bat   Batch mode for plot. Otherwise interactive. (default: False)

Program flow¶

extract_desired_criteria: Extract desired refinement criteria
launch_segrefine3dcyclexplore_gui: Explore different refinement criteria interactively

Functions¶

Documented functions with links to source