.. _segmentexam: Segmentexam ----------- Program to examine all excised in-plane rotated segments and compute their collapsed (1D) and 2D power spectrum and width profile of helices +--------------------------------------------------+--------------------------------------------------+ | |segmentexam_input.png| | |segmentexam_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Image input stack | Output: Diagnostic plot | +--------------------------------------------------+--------------------------------------------------+ .. |segmentexam_input.png| image:: ../gallery_images/segmentexam_input.png :alt: tree :width: 4 cm :target: ../_images/segmentexam_input.png .. |segmentexam_output.png| image:: ../gallery_images/segmentexam_output.png :alt: tree :width: 4 cm :target: ../_images/segmentexam_output.png .. _making_a_segmentexam_table_for_beginner: Parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Image input stack protein_stack.hdf Input stack: accepted file formats (hdf). Diagnostic plot segmentexam_diag.pdf Output diagnostic plot: accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff). Power spectrum output image power.hdf Output power spectrum image: accepted file formats (hdf). Pixel size in Angstrom 1.163 Pixel size is an imaging parameter (accepted values min=0.001, max=100). Estimated helix width in Angstrom 200 Generous width measure of helix required for rectangular mask (accepted values min=0, max=1500). spring.db file spring.db Program requires a combined spring.db from segment (and optional: micctfdetermine). An updated spring.db will be created in the working directory. ============================================================================== ============================================================================== ==================================================================================================== .. _segmentexam_parameter_file_for_beginner: Sample parameter file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: segmentexam --f parameterfile.txt Where the format of the parameters is:: Image input stack = protein_stack.hdf Diagnostic plot = segmentexam_diag.pdf Power spectrum output image = power.hdf Pixel size in Angstrom = 1.163 Estimated helix width in Angstrom = 200 spring.db file = spring.db .. _making_a_segmentexam_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== MPI option True OpenMPI installed (mpirun). Number of CPUs 8 Number of processors to be used (accepted values min=1, max=1000). Temporary directory /tmp Temporary directory should have fast read and write access. ============================================================================== ============================================================================== ==================================================================================================== .. _segmentexam_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:: segmentexam --f parameterfile.txt Where the format of the parameters is:: Image input stack = protein_stack.hdf Diagnostic plot = segmentexam_diag.pdf Power spectrum output image = power.hdf Pixel size in Angstrom = 1.163 Estimated helix width in Angstrom = 200 spring.db file = spring.db MPI option = True Number of CPUs = 8 Temporary directory = /tmp .. _making_a_segmentexam_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Enhanced power spectrum option True Option to enhance power spectrum to compensate for decay of amplitudes. Enhanced power spectrum output image power_enhanced.hdf Output enhanced power spectrum image (compensated for decay of amplitudes): accepted file formats (hdf). Power spectrum resolution cutoff in 1/Angstrom 0.15 Images are binned to obtain a suitable power spectrum (accepted values min=0, max=1). Compute layer-line correlation option False Compute layer line correlation of individual power spectra with average power spectrum and store this correlation value in the Spring database (spring.db). Layer-line region in 1/Angstrom (0.03, 0.035) Layer-line region to correlate individual power spectrum with sum of all power spectra (accepted values min=0, max=1). Reference power spectrum False Choose whether to provide a reference power spectrum for layer-line correlation. Make sure that the image dimensions agree with the input stack or with the binned input stack. If not chosen, sum of power spectra from input stack will be used. Power spectrum input image power.hdf Input power spectrum image: accepted file formats (hdf). Micrographs select option False Choose whether to select any particular micrographs. Include or exclude micrographs include Choose whether to 'include' or 'exclude' specified micrographs. Micrographs list 1-9, 11, 13 List of comma-separated micrograph ids, e.g. '1-10, 12, 14' (1st micrograph is 1). Helices select option False Choose whether to select any particular helices. Include or exclude helices include Choose whether to 'include' or 'exclude' specified helices. Helices list 1-9, 11, 13 List of comma-separated helix ids, e.g. '1-10, 12, 14' (1st helix is 1). Segments select option False Choose whether to select any particular segments. Include or exclude segments include Choose whether to 'include' or 'exclude' specified segments. Segment file stackid_file.dat File with single column of stack_ids. Classes select option False Choose whether to select any particular classes. Include or exclude classes include Choose whether to 'include' or 'exclude' specified classes. Class type class_id Choose class type either 'class_id' based on segmentclass assignments or 'class_model_id' based on segmultirefine3d/segclassmodel assigments. Classes list 1-9, 11, 13 List of comma-separated class ids, e.g. '1-10, 12, 14' (1st class is 0). Persistence class option False Choose whether to select segments from classes based on class assignments of neighboring segments. Persistence class length in Angstrom 700 Length of helix window that will be used to average the class memberships of segments (accepted values min=1, max=5000). Class occupancy threshold 0.5 Class occupancy threshold of segments (between 0 and 1) that belong to specified subset of classes within persistence length. Segments that have a lower occupancy will be excluded (accepted values min=0, max=1). Straightness select option False Choose whether to select any helices based on straightness. Include or exclude straight helices include Choose whether to 'include' or 'exclude' helices of specified persistence length. Persistence length range (80, 100) Range of persistence length in percent, i.e. upper 10 percent of distribution is expressed as 90 - 100 percent range, lower 20 percent is expressed as 0 - 20 percent etc. 90 - 100 % corresponds to most straight helices. Values from database are stored in m, e.g. '0-0.0001' Persistence length is calculated as: p = -ln(2 * (end_to_end_distance / contour_length) ** 2 - 1) / contour_length)), i.e. short persistence lengths of 1 nm correspond to very flexible whereas 1 m corresponds to extremely straight helices. Examples are TMV: 2.9 mm (2.9e-3 m), amyloid beta filaments: 300 microm (3e-4 m) and DNA: 100 nm (1e-7 m). Due to the alignment error of the segments this value may not be absolutely comparable to determined persistence lengths by other methods but still be valid as a relative measure of straightness (accepted values min=0, max=100). Layer line correlation select option False Choose whether to select any segments based on layer-line cross-correlation coefficient. Include or exclude segments based on layer-line correlation include Choose whether to 'include' or 'exclude' segments of specified cross correlation coefficient with layer lines. Correlation layer line range (60, 100) Range of cross-correlation between layer lines of power spectrum average and segment in percent. i.e. upper 10 percent of distribution is expressed as 90 - 100 percent range, lower 20 percent is expressed as 0 - 20 percent etc. Values in database are stored as cross correlation coefficient, e.g. '0.5 - 1.0' (accepted values min=0, max=100). Defocus select option False Choose whether to select any segments based on defocus. Include or exclude defocus range include Choose whether to 'include' or 'exclude' segments of specified defocus. Defocus range (10000, 40000) Range of defocus in Angstrom, e.g. '10000-40000' (accepted values min=0, max=100000). Astigmatism select option False Choose whether to select any segments based on astigmatism. Include or exclude astigmatic segments include Choose whether to 'include' or 'exclude' segments of specified astigmatism amplitude in Angstrom. Astigmatism range (0, 4000) Range of astigmatism amplitude (difference between defocus one and two) in Angstrom, e.g. '0-4000' (accepted values min=0, max=100000). ============================================================================== ============================================================================== ==================================================================================================== .. _segmentexam_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:: segmentexam --f parameterfile.txt Where the format of the parameters is:: Image input stack = protein_stack.hdf Diagnostic plot = segmentexam_diag.pdf Power spectrum output image = power.hdf Enhanced power spectrum option = True Enhanced power spectrum output image = power_enhanced.hdf Pixel size in Angstrom = 1.163 Estimated helix width in Angstrom = 200 Power spectrum resolution cutoff in 1/Angstrom = 0.15 Compute layer-line correlation option = False Layer-line region in 1/Angstrom = (0.03, 0.035) Reference power spectrum = False Power spectrum input image = power.hdf spring.db file = spring.db Micrographs select option = False Include or exclude micrographs = include Micrographs list = 1-9, 11, 13 Helices select option = False Include or exclude helices = include Helices list = 1-9, 11, 13 Segments select option = False Include or exclude segments = include Segment file = stackid_file.dat Classes select option = False Include or exclude classes = include Class type = class_id Classes list = 1-9, 11, 13 Persistence class option = False Persistence class length in Angstrom = 700 Class occupancy threshold = 0.5 Straightness select option = False Include or exclude straight helices = include Persistence length range = (80, 100) Layer line correlation select option = False Include or exclude segments based on layer-line correlation = include Correlation layer line range = (60, 100) Defocus select option = False Include or exclude defocus range = include Defocus range = (10000, 40000) Astigmatism select option = False Include or exclude astigmatic segments = include Astigmatism range = (0, 4000) MPI option = True Number of CPUs = 8 Temporary directory = /tmp .. _using_segmentexam_on_cmdline: Command line options ~~~~~~~~~~~~~~~~~~~~~~~ When invoking segmentexam, you may specify any of these options:: usage: segmentexam [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--enhanced_power_spectrum_option] [--compute_layer-line_correlation_option] [--reference_power_spectrum] [--micrographs_select_option] [--helices_select_option] [--segments_select_option] [--classes_select_option] [--persistence_class_option] [--straightness_select_option] [--layer_line_correlation_select_option] [--defocus_select_option] [--astigmatism_select_option] [--mpi_option] [input_output [input_output ...]] Program to examine all excised in-plane rotated segments and compute their collapsed (1D) and 2D power spectrum and width profile of helices 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 --enhanced_power_spectrum_option, --enh Option to enhance power spectrum to compensate for decay of amplitudes. (default: False) --compute_layer-line_correlation_option, --com Compute layer line correlation of individual power spectra with average power spectrum and store this correlation value in the Spring database (spring.db). (default: False) --reference_power_spectrum, --ref Choose whether to provide a reference power spectrum for layer-line correlation. Make sure that the image dimensions agree with the input stack or with the binned input stack. If not chosen, sum of power spectra from input stack will be used. (default: False) --micrographs_select_option, --mic Choose whether to select any particular micrographs. (default: False) --helices_select_option, --hel Choose whether to select any particular helices. (default: False) --segments_select_option, --seg Choose whether to select any particular segments. (default: False) --classes_select_option, --cla Choose whether to select any particular classes. (default: False) --persistence_class_option, --per Choose whether to select segments from classes based on class assignments of neighboring segments. (default: False) --straightness_select_option, --str Choose whether to select any helices based on straightness. (default: False) --layer_line_correlation_select_option, --lay Choose whether to select any segments based on layer-line cross-correlation coefficient. (default: False) --defocus_select_option, --def Choose whether to select any segments based on defocus. (default: False) --astigmatism_select_option, --ast Choose whether to select any segments based on astigmatism. (default: False) --mpi_option, --mpi OpenMPI installed (mpirun). (default: False) Program flow ~~~~~~~~~~~~~~~~~~~~ #. add_power_spectra_from_verticalized_stack: Addition of in-plane rotated power spectra #. determine_width: Determine width of helix by projection along helical axis #. visualize_power_avg_and_width_analysis: Visualization of width and power spectra Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 segmentexam_functions