.. _segclasslayer: Segclasslayer ------------- Program to extract amplitudes and phases from desired layer lines of class averages +--------------------------------------------------+--------------------------------------------------+ | |segclasslayer_input.png| | |segclasslayer_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Class average stack | Output: Interactive screenshot | +--------------------------------------------------+--------------------------------------------------+ .. |segclasslayer_input.png| image:: ../gallery_images/segclasslayer_input.png :alt: tree :width: 4 cm :target: ../_images/segclasslayer_input.png .. |segclasslayer_output.png| image:: ../gallery_images/segclasslayer_output.png :alt: tree :width: 4 cm :target: ../_images/segclasslayer_output.png .. _making_a_segclasslayer_table_for_beginner: Parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Class average stack avgerages.hdf Class average stack: accepted file formats (hdf). Batch mode False Batch mode for plot. Otherwise interactive. Diagnostic plot segclasslayer_diag.pdf Output diagnostic plot: accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff). Class format real Choose whether class average stack is in real or power spectrum format. Pixel size in Angstrom 1.163 Pixel size is an imaging parameter (accepted values min=0.001, max=100). Precise helix width in Angstrom 180 Precise width of helix for layer line interpretation (accepted values min=20, max=1500). Class number range to be analyzed (3, 5) Class number range to be analyzed (1st class is 0) (accepted values min=0, max=2000). ============================================================================== ============================================================================== ==================================================================================================== .. _segclasslayer_parameter_file_for_beginner: Sample parameter file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: segclasslayer --f parameterfile.txt Where the format of the parameters is:: Class average stack = avgerages.hdf Batch mode = False Diagnostic plot = segclasslayer_diag.pdf Class format = real Pixel size in Angstrom = 1.163 Precise helix width in Angstrom = 180 Class number range to be analyzed = (3, 5) .. _making_a_segclasslayer_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== ============================================================================== ============================================================================== ==================================================================================================== .. _segclasslayer_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:: segclasslayer --f parameterfile.txt Where the format of the parameters is:: Class average stack = avgerages.hdf Batch mode = False Diagnostic plot = segclasslayer_diag.pdf Class format = real Pixel size in Angstrom = 1.163 Precise helix width in Angstrom = 180 Class number range to be analyzed = (3, 5) .. _making_a_segclasslayer_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== B-Factor 0 B-Factor in 1/Angstrom^2 to be applied to images. Zero no modulation of frequencies. Negative B-factors enhance high-resolution frequencies. Positive B-factors dampen high-resolution frequencies (accepted values min=-50000, max=50000). Power spectrum resolution cutoff in 1/Angstrom 0.15 Images are binned to obtain a suitable power spectrum (accepted values min=0, max=1). Layer line positions 0.1234,0.234 List of comma-separated values in reciprocal Angstrom Pad option True If layer lines are part of a continuous lattice set, average will be padded so that layer lines lie exactly on pixel grid ============================================================================== ============================================================================== ==================================================================================================== .. _segclasslayer_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:: segclasslayer --f parameterfile.txt Where the format of the parameters is:: Class average stack = avgerages.hdf Batch mode = False Diagnostic plot = segclasslayer_diag.pdf Class format = real Pixel size in Angstrom = 1.163 Precise helix width in Angstrom = 180 B-Factor = 0 Power spectrum resolution cutoff in 1/Angstrom = 0.15 Class number range to be analyzed = (3, 5) Layer line positions = 0.1234,0.234 Pad option = True .. _using_segclasslayer_on_cmdline: Command line options ~~~~~~~~~~~~~~~~~~~~~~~ When invoking segclasslayer, you may specify any of these options:: usage: segclasslayer [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--batch_mode] [--pad_option] [input_output [input_output ...]] Program to extract amplitudes and phases from desired layer lines of class averages 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) --pad_option, --pad If layer lines are part of a continuous lattice set, average will be padded so that layer lines lie exactly on pixel grid (default: False) Program flow ~~~~~~~~~~~~~~~~~~~~ #. extract_layerlines: Extracts layer lines from specified position #. visualize_layerlines: Visualization of layer lines Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 segclasslayer_functions