Segclasslayer¶

Program to extract amplitudes and phases from desired layer lines of class averages

Input: Class average stack

Output: Interactive screenshot

Parameters¶

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).

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)

Additional parameters (intermediate level)¶

Parameter	Example (default)	Description

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)

Additional parameters (expert level)¶

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

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

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¶

Documented functions with links to source