.. _segrefine3dcyclexplore: Segrefine3dcyclexplore ---------------------- Program to interactively explore refinement cycle statistics +--------------------------------------------------+--------------------------------------------------+ | |segrefine3dplot_output.png| | |segrefine3dcyclexplore_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: refinement.db file | Output: Interactive screenshot | +--------------------------------------------------+--------------------------------------------------+ .. |segrefine3dplot_output.png| image:: ../gallery_images/segrefine3dplot_output.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dplot_output.png .. |segrefine3dcyclexplore_output.png| image:: ../gallery_images/segrefine3dcyclexplore_output.png :alt: tree :width: 4 cm :target: ../_images/segrefine3dcyclexplore_output.png .. _making_a_segrefine3dcyclexplore_table_for_beginner: Parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== 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. ============================================================================== ============================================================================== ==================================================================================================== .. _segrefine3dcyclexplore_parameter_file_for_beginner: 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 .. _making_a_segrefine3dcyclexplore_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== 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; ============================================================================== ============================================================================== ==================================================================================================== .. _segrefine3dcyclexplore_parameter_file_for_intermediate: 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 .. _making_a_segrefine3dcyclexplore_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== ============================================================================== ============================================================================== ==================================================================================================== .. _segrefine3dcyclexplore_parameter_file_for_expert: 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 .. _using_segrefine3dcyclexplore_on_cmdline: 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 ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 segrefine3dcyclexplore_functions