siroccomol

Render proteins as space-filling molecular surfaces in two styles.

• matte: flat diffuse shading with soft cast shadows and dark silhouette and crevice contours (Goodsell-inspired).
• cel: saturated, posterized anime cel shading with crisp flat cast shadows, cool shadow tones, a warm highlight and a rim light (similar to a well known illustration style optional sky-gradient backdrop via sky).

A protein's atoms sit at bond distances, so the renderer builds a smooth isosurface over them, ray-marches it on the GPU, shades it, and inks the contours. It runs headless through EGL.

The name is a nod to the sirocco, the hot Mediterranean wind.

Gallery

GroEL/GroES chaperonin · 1AON, video

20S proteasome · 1PMA, video

SARS-CoV-2 spike · 6VXX, video

Immunoglobulin · 1IGT, video

Haemoglobin · 4HHB, video

Green fluorescent protein · 1GFL, video

Install

uv pip install siroccomol

Needs a GPU with a headless GL/EGL driver (NVIDIA with libEGL, or Mesa), and ffmpeg for the spin videos.

Use

A PDB id is fetched from RCSB automatically.

siroccomol 4HHB --style cel -o hemoglobin.png
siroccomol 4HHB --compare -o compare.png
siroccomol 4HHB --spin --compare -o compare.mp4
siroccomol 4HHB --spin -o spin.mp4 --frames 120 --px 1080 --ss 3   # high-quality video
siroccomol my_structure.pdb --color-by element --px 1600

import siroccomol

siroccomol.render_protein("4HHB", style="cel", out="hemoglobin.png")
siroccomol.compare("4HHB", out="compare.png")
siroccomol.compare_spin("4HHB", out="compare.mp4")
siroccomol.spin("4HHB", out="spin.mp4", frames=120, px=1080, ss=3)
img = siroccomol.render_protein("1UBQ", style="matte")

Options

spin and compare_spin encode a high-quality H.264 video (.mp4/.mov/.mkv), which needs ffmpeg on PATH. Good quality settings are frames=120, fps=30, px=1080, ss=3, crf=17 (Python only).

How it works

1. Voxelize the atoms into a density field plus a smooth per-voxel colour, in a grid aligned to the structure's principal axes. Exposed atoms get a saturation boost first, so terminal side-chain bumps pop (Goodsell-style).
2. Ray-march the density = iso isosurface on the GPU.
3. Shade from the surface normal (the density gradient), and cast a shadow ray through the volume toward the light. Matte is diffuse with a soft shadow; cel is a saturated 4-tone with a crisp flat shadow and rim light.
4. A contour pass inks the silhouette, the occluding depth edges and the colour boundaries, with the line width scaled to the structure's feature size.

For animation the volume is built once and the camera orbits per frame.

Thanks

The shader I used is based on ghibli-style-shader by the brilliant craftzdog.

MIT licensed. The official illustrations in gallery/goodsell/ are by David S. Goodsell and the RCSB PDB, from PDB-101 Molecule of the Month, used under CC-BY-4.0.