Methods and sources

Every molecule on this site comes from atomic coordinates in the Protein Data Bank. This page states what the site measures, what it interpolates and what it draws by hand.

Structures

The atlas lists 193 PDB entries. The RCSB API supplied the title, method, resolution, chain names and primary citation of each one. The 3D views use 90 of them. A build script reads each mmCIF file and keeps the heavy atoms of the first model. It writes two sphere sets: one sphere per atom, and one per residue for large assemblies. Titles, organisms, resolutions and citations on each page come from the same files.

Drawing style

The renderer draws each atom as a ray-traced sphere on the GPU, so a million spheres cost one draw call per part. A second pass adds dark contour lines where depth jumps, thinner lines between chains, soft ambient occlusion and a gentle fade with distance. The flat pastel palette follows the illustrative style that David Goodsell uses for molecules. The site has no affiliation with him.

Animations

Most mechanisms morph between solved conformations of the same protein (5 morph sets). The build script superposes each state on a stable core with an iterative fit. It matches atoms by chain, residue number and atom name, then stores the coordinates. The browser interpolates in straight lines, so the path between two states is drawn, not measured. Atoms missing from one state shrink away instead of jumping.

Rigid turns use axes measured from the structures. In ATP synthase the rotor turns about the line from the c-ring to the α3β3 head. The three rotary states of the human enzyme give the direction of synthesis. In the flagellar motor, the filament grows by repeating the flagellin-to-flagellin screw measured in the hook-filament junction entry. In kinesin, the microtubule lattice uses the tubulin frame of the kinesin-tubulin complex and standard 13-protofilament geometry.

Modelled, not measured

Lipid bilayers, the peptidoglycan wall, cargo vesicles, protons and free nucleotides are simple beads.
The kinesin neck linkers, the coiled-coil stalk and the GroEL client protein are illustrative bead chains.
Stator-unit positions in the flagellar motor, and membrane positions of pumps, are estimates from structure and hydrophobicity.
Each swapped part in the labs sits on the axis of the part it replaces. The site never predicts whether a swap folds or works. It reports what a cited experiment found.
The animations run slow, so each step stays visible. Real machines run hundreds of times faster.
The cell landscape on the home page is a composite for illustration, not a model of a real cell.

Text and citations

Numbers and mechanism claims carry numbered citations. Crossref confirmed every DOI, and the paper abstract confirmed most claims. The page leaves out any value that failed this check.

Data

Coordinates come from the RCSB Protein Data Bank, part of the wwPDB. Cite the original structure papers. Each machine page lists them under Sources.