Drybench Cell.

A guided tour of how a human cell turns a gene into a working protein, in eight steps: DNA packed in chromatin, transcription by RNA polymerase II, splicing, export from the nucleus, translation on the ribosome, the new chain in the exit tunnel, folding inside a chaperonin, and a finished protein, haemoglobin, at work.

Each step is a real structure from the Protein Data Bank, determined by X-ray crystallography or cryo-electron microscopy, with its primary paper. The colours mean the same thing in every step: DNA, messenger RNA, other RNAs, the protein machinery, the protein being made and small molecules.

The page ships the tour text and a still image for each step. The 3D view loads only when you ask for it: first the Mol* viewer (about 1.5 MB compressed), then, for each step, a gzipped BinaryCIF structure file of 25 to 240 KB (60 to 420 KB unzipped) and a MolViewSpec scene that sets the representation, colours, labels, cutaway plane and camera. The page downloads and unzips each file itself, so a download for a step you have already left is cancelled, and a stalled one ends with a message and a retry.

The structure files are cut down from the PDB entries by the build pipeline to the atoms shown, with no water or hydrogens. For the five biggest complexes by atom count, the spliceosome, TREX, the two ribosomes and TRiC, with about 36,000 to 215,000 atoms each, the machinery keeps one atom per residue and is drawn as a backbone trace, while the RNAs and chains the step is about keep every atom. That keeps them usable on a phone.

A Python pipeline checks every PDB entry against the RCSB Data API (title, organism, method, resolution, year), checks each primary citation against Europe PMC, and checks UniProt accessions. It then reads the structures with Biotite, confirms each coloured entity is what the scene says it is, measures the numbers the text quotes with NumPy and SciPy (sizes, resolved residues, base pairs, how far the chain in the tunnel reaches from its tRNA), works out the camera and cutaway plane, and writes the trimmed, gzipped files and the scene data, noting which revision of each entry they were cut from.

The stills were rendered headless in Blender 5.2 with the Molecular Nodes add-on, using Cycles on the CPU with 32 samples and denoising. The render script reads the same scene data as the 3D viewer, so each still shows the same structure, colours, cutaway and viewing direction. The stills are the step images before the 3D view loads, and the fallback where WebGL is not available.