Simulate Tomograms

cylindra implements several methods to simulate cylindric structures.

GUI: Image > Simulate cylindric structure or Ctrl+K → I

The simulator widget is available at ui.simulator.

Prepare a spline with arbitrary shape

Before running simulation, you have to place molecules at the desired positions and orientations. To do this, you can first create an empty image, and draw splines of any shape on it.

API: create_empty_image

GUI: Simulator widget > Create > Create empty image

create_empty_image

The image size and the pixel scale will be directly used as the simulated tomograms.

Note

You can also call mapping functions on splines tagged with helical parameters measured by CFT.

Simulate cylinder with constant periodicity

API: generate_molecules

GUI: Simulator widget >

With spline-to-molecules mapping functions, the molecules were initialized based on the helical parameters of the spline. Instead of referring to the measured parameters, you can generate molecules along the spline with arbitrary parameters. Following GIF shows how to adjust parameters while previewing the result.

generate_molecules

The generated molecules will be added to the viewer with some names like Mole(Sim)-0.

Apply local conformational changes to molecules

The method above can only generate molecules with constant parameters. To simulate local conformational changes, you can use the following method. Common parameters are:

by: the amount of change.
yrange: the longitudinal range of the local region. yrange=(5, 10) means that the 5th molecules to the 9th (end excluded!) molecules from the edge will be affected.
arange: the lateral range of the local region. arange=(2, 5) means that the molecules in the 2nd to 4th (end excluded!) protofilaments will be affected.

and the preview is also available.

Local expansion/compaction

API: expand

GUI: Simulator widget > expand

Programatically apply local expansion

This script will expand the 10th to 20th molecules (all the protofilaments) from the tip in the layer named "Mole(Sim)-0" by 0.1 nm.

ui.simulator.expand("Mole(Sim)-0", by=0.1, yrange=(10, 20))

Local twisting

API: twist

GUI: Simulator widget > twist

Local dilation

API: dilate

GUI: Simulator widget > dilate

Define conformational changes by expressions

API: displace

GUI: Simulator widget > displace

simulate supertwist

After seam-searching, column "isotype-id" will be added to the molecules layer, which indicates the alpha/beta isotype of each molecule.

dtheta = 0.05
ui.simulator.displace(
    layer="Mole(Sim)-0",
    twist=pl.when(pl.col("isotype-id").eq(1)).then(-dtheta).otherwise(dtheta)
)

Asign Density to Molecules

API: add_component

GUI: Simulator widget > add_component

Note

Before this step, you can run any operations on the molecules, such as filtration and split/combine.

Once the molecules are ready, you have to assign a template image to each molecules layer for simulation. In this method, you can select image files and assign them to one of the molecules layers in the viewer. The image don't have to be scaled; it will automatically be rescaled to the pixel scale of the tomogram.