My colleagues recently published a paper (Nakane et al. (2020) “Single Particle cryo-EM at atomic resolution”) and asked me to make a figure. I did so and it is this week’s front cover image.

This was made with the “gtk3” branch of Coot.

Apoferritin small image

High resolution version:

For radial colouring I used something like:

coot.set_draw_solid_density_surface(imol_map, 1)
coot.set_radial_map_colouring_min_radius(imol_map, 20)
coot.set_radial_map_colouring_max_radius(imol_map, 80)
coot.set_radial_map_colouring_invert(imol_map, 1)
coot.set_radial_map_colouring_enabled(imol_map, 1)

Takanori himself made a front cover image too in PyMOL and seeing that I tried to make a version in a similar style using Coot. I didn’t copy it exactly, you can see that my version is not volumetric and is smoother and more gem-like.

Apoferritin Hydrogen Atom Density small image

The point of this image is to illustrate that the reconstruction provides good evidence for the position of hydrogen atoms (which are the green blobs, of course).

High resolution version: This is intentionally large, to demonstrate the arbitrary framebuffer scaling.

You can see Takanori’s version on twitter (he is @biochem_fan)

The source code for “gtk3” Coot is updated/released every day or so, but the binaries are not (that’s too much of a time sink at the moment).

Here’s the script to make that second image:

import coot

b_factor = 1
resample_factor =  1.9

f1 = 0.0

imol = read_pdb("ref1_n1_hydr_aniso_p-chainAL-HOH302.pdb")
coot.set_rotation_centre(65, 26, 32)
coot.set_bond_thickness(imol, 4)

imol_map      = coot.handle_read_ccp4_map('apoF/aroundW302-normal.ccp4', 0)
imol_diff_map = coot.handle_read_ccp4_map('apoF/aroundW302-diff.ccp4',   0) # naughty

imol_map      = coot.sharpen_blur_map_with_resampling(imol_map,      b_factor, resample_factor);
imol_diff_map = coot.sharpen_blur_map_with_resampling(imol_diff_map, b_factor, resample_factor);

coot.set_draw_solid_density_surface(imol_map, 1)
coot.set_draw_solid_density_surface(imol_diff_map, 1)

coot.set_solid_density_surface_opacity(imol_map,      0.5);
coot.set_solid_density_surface_opacity(imol_diff_map, 0.5);

imol_map_copy      = coot.copy_molecule(imol_map)
imol_diff_map_copy = coot.copy_molecule(imol_diff_map)

coot.set_map_colour(imol_map,      0.1, 0.1, 0.5)
coot.set_map_colour(imol_diff_map, 0.2, 0.4, 0.2)
coot.set_map_colour(imol_map_copy,      0.4, 0.4, 0.9)
coot.set_map_colour(imol_diff_map_copy, 0.4, 0.7, 0.4)

coot.set_draw_solid_density_surface(imol_map_copy, 1)
coot.set_draw_solid_density_surface(imol_diff_map_copy, 1)

coot.set_solid_density_surface_opacity(imol_map_copy,      0.15);
coot.set_solid_density_surface_opacity(imol_diff_map_copy, 0.15);

coot.set_map_material_specular(imol_map, 10, 100)
coot.set_map_material_specular(imol_diff_map, 10, 100)

coot.set_contour_level_absolute(imol_map, 0.135)
coot.set_contour_level_absolute(imol_map_copy, 0.208)
coot.set_contour_level_absolute(imol_diff_map, 0.155)
coot.set_contour_level_absolute(imol_diff_map_copy, 0.26)

I applied the blur using the GIMP because Coot’s blur filter is not very good at the moment.