Microtubule for Figures

Drawing a microtubule for figures (e.g., for a PowerPoint presentation) is not easy. You usually need to carefully place tubulins so that it looks real. The z-order of tubulins is also important but it is hard to manage.

The simulator widget is useful for this purpose.

Draw a spline

First, draw a spline that represents the microtubule.

Create an empty image and draw manually

API: create_empty_image

GUI: Simulator widget > Create > Create empty image

Create an image with a straight line

API: create_image_with_straight_line

GUI: Simulator widget > Create > Create image with straight line

ui.simulator.create_empty_image(size=(60.0, 80.0, 80.0), scale=0.5)
ui.register_path(coords=[[30, -157, 5], [30, -82, 30], [30, -11, 13], [30, 62, 39]])

Generate tubulins

Once splines are drawn, you can generate tubulins along the spline.

ui.simulator.generate_molecules(spline=0, spacing=4.08, twist=0.04, start=3, npf=13, radius=10.0)

You can also adjust the point size and the view mode from the layer control. In the napari file menu, you can copy or save the screenshot of the current view.

make_figure

Color by α- and β-tubulins

Manual seam-searching can be used for coloring tubulins.

ui.sta.seam_search_manually("Mole(Sim)-0")  # assign 0 and 1 to tubulins
ui.paint_molecules("Mole(Sim)-0", color_by="isotype-id", cmap={0: "#A2A2A2", 1: "#FFE2E2"}, limits=(0, 1))