Segrefine3dplot¶

Program to plot refinement parameters from segmentrefine3d

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.
spring.db file	spring.db	Requires spring.db from segment to plot helix parameters.
Refinement quantities	coordinates	Refinement quantities to be plotted: ‘coordinates’: Refined X-Coordinate (Angstrom) vs. Refined Y-Coordinate (Angstrom); Picked X-Coordinate (Angstrom) vs. Picked X-Coordinate (Angstrom); ‘coordinates_subunit’: Refined Subunit X-Coordinate (Angstrom) vs. Refined Subunit Y-Coordinate (Angstrom); Picked X-Coordinate (Angstrom) vs. Picked X-Coordinate (Angstrom); ‘in-plane_rotation’: Distance Along Helix (Angstrom) vs. In-Plane Rotation Angle (Degrees) (Distance Along Helix (Angstrom) of segment center from helix start, In-Plane Rotation Angle (Degrees) of segment based on projection matching); ‘normalized_in-plane_rotation’: Distance Along Helix (Angstrom) vs. Normalized In-Plane Rotation Angle (Degrees) (Distance Along Helix (Angstrom) of segment center from helix start, Normalized In-Plane Rotation Angle (Degrees) of segment based on projection matching (orientation derived from picked coordinates is zero)); ‘phi’: Distance Along Helix (Angstrom) vs. Phi (Degree) (Distance Along Helix (Angstrom) of segment center from helix start, Phi (Degree) assigned Euler angle of segment); ‘theta’: Distance Along Helix (Angstrom) vs. Theta (Degree) (Distance Along Helix (Angstrom) of segment center from helix start, Theta (Degree) assigned Euler angle of segment); ‘psi’: Distance Along Helix (Angstrom) vs. Psi (Degree) (Distance Along Helix (Angstrom) of segment center from helix start, Psi (Degree) assigned Euler angle of segment); ‘x_shift’: Distance Along Helix (Angstrom) vs. X-Shift (Angstrom) (Distance Along Helix (Angstrom) of segment center from helix start, X-Shift (Angstrom) of image required for transformation and insertion of image into 3D reconstruction); ‘y_shift’: Distance Along Helix (Angstrom) vs. Y-Shift (Angstrom) (Distance Along Helix (Angstrom) of segment center from helix start, Y-Shift (Angstrom) of image required for transformation and insertion of image into 3D reconstruction); ‘shift_perpendicular_to_helix’: Distance Along Helix (Angstrom) vs. Helix Shift Perpendicular (Angstrom) (Distance Along Helix (Angstrom) of segment center from helix start, Helix Shift Perpendicular (Angstrom) of image perpendicular to helix axis); ‘shift_along_helix’: Distance Along Helix (Angstrom) vs. Helix Shift Parallel (Angstrom) (Distance Along Helix (Angstrom) of segment center from helix start, Helix Shift Parallel (Angstrom) of image along helix axis);

Sample parameter file¶

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

segrefine3dplot --f parameterfile.txt

Where the format of the parameters is:

refinement.db file                       = refinement.db
Batch mode                               = False
spring.db file                           = spring.db
Refinement quantities                    = coordinates

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).

Sample parameter file (intermediate level)¶

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

segrefine3dplot --f parameterfile.txt

Where the format of the parameters is:

refinement.db file                       = refinement.db
Batch mode                               = False
Diagnostic plot prefix                   = diagnostic_plot.pdf
spring.db file                           = spring.db
Refinement quantities                    = coordinates

Additional parameters (expert level)¶

Parameter	Example (default)	Description
Set size	helix	Choose set size to plot: chosen quantity per ‘helix’, ‘micrograph’ or ‘data_set’.
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).

Sample parameter file (expert level)¶

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

segrefine3dplot --f parameterfile.txt

Where the format of the parameters is:

refinement.db file                       = refinement.db
Batch mode                               = False
Diagnostic plot prefix                   = diagnostic_plot.pdf
spring.db file                           = spring.db
Refinement quantities                    = coordinates
Set size                                 = helix
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

Command line options¶

When invoking segrefine3dplot, you may specify any of these options:

usage: segrefine3dplot [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--batch_mode]
                       [--micrographs_select_option] [--helices_select_option]
                       [input_output [input_output ...]]

Program to plot refinement parameters from segmentrefine3d

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)
  --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)

Program flow¶

get_ref_quantities_per_set: Extract desired refinement quantities from spring database
plot_data_on_figure: Prepare figures with desired refined quantities

Functions¶

Documented functions with links to source