Spline Configurations

A spline is tagged with a SplineConfig object. This object is practically used to annotate the spline with structural features. For example, if a spline represent a microtubule, it is tagged with a SplineConfig object with parameters appropriate for microtubules. These parameters are used in spline fitting, CFT analysis, and so on.

Every time a new spline is created, it is initialized with the default SplineConfig. Make sure the correct configuration is used before adding splines.

List of Parameters

• Parameters used during CFT analysis
• npf_range ... an (int, int) tuple indicating the minimum/maximum of the number of protofilaments.
• spacing_range ... an (float, float) tuple indicating the minimum/maximum of longitudinal spacing between monomers (in nanometer).
• twist_range ... an (float, float) tuple indicating the minimum/maximum of twist angle (in degree).
• rise_range ... an (float, float) tuple indicating the minimum/maximum of rise angle (in degree).

• rise_sign ... the sign of the rise angle. This parameter is redundant for the mathematically. It was introduced only to make the rise angle and the start number positive, like "13_3" instead of "13_-3".

• Other parameters

• clockwise ... "PlusToMinus" or "MinusToPlus". This parameter is used for automatic polarity determination. If the cross-sectional view of the cylindric structure in the plus-to-minus orientation has clockwise chirality, set this parameter to "PlusToMinus".
• thickness_inner ... distance between the inner surface and the peak of the radial profileradius (in nanometer). This parameter is used for construction of cylindric coordinate system.
• thickness_inner ... distance between the outer surface and the peak of the radial profileradius (in nanometer). This parameter is used for construction of cylindric coordinate system.
• fit_depth ... the depth of sub-volumes used for spline fitting region (in nanometer).
• fit_width ... the width of sub-volumes used for spline fitting region (in nanometer).

Change the Default Configuration

The configuration is optimized for microtubules by default. To analyze other structures, you need to change the default configuration.

The default configuration is stored in the default_config property.

ui.default_config

Output

SplineConfig(
    npf_range=Range(min=11, max=17),
    spacing_range=Range(min=3.9, max=4.3),
    twist_range=Range(min=-0.65, max=0.65),
    rise_range=Range(min=5.0, max=13.0),
    rise_sign=-1,
    clockwise='MinusToPlus',
    thickness_inner=2.8,
    thickness_outer=2.8,
    fit_depth=49.0,
    fit_width=40.0
)

Manually set the parameters

GUI: Splines > Config > Update default config

Measuring the approximate parameters of unknown structures

GUI: Analysis > Open spectra inspector

The widget for inspecting the power spectrum of the spline can also be used to measure lattice parameters. After enabling "Select axial peak" mode, you can manally select the peak position to measure the lattice parameters. After selecting the axial peak, you can then "Select angular peak".

Load presets

GUI: Splines > Config > Load default config

Presets are stored in the user directory. You can load the presets from the menu.

By default, presets for following biological components are available:

• F-actin
• Eukaryotic microtubule
• BtubAB (a bacterial microtubule)
• Tobacco mosaic virus

Save the Configuration

GUI: Splines > Config > Save default config

You can save current default configuration as a preset with arbitrary name.