NotMarbles
Also: NotOrigami, is a protein folded like origami? Paper, protein or both.
Draw a protein as space-filling spheres and it looks like a solid pile of hard, fixed marbles. It isn’t. Every atom is jiggling all the time, and some parts of a protein move far more than others. In this game you bet which regions hold their place and which smear — then watch the mobile ones jitter. Everything runs locally; nothing about you is collected.
This is the tool — a small game, no login, nothing tracked. Every protein and its regions are listed in full below (works without JavaScript). Motion respects your “reduce motion” setting.
Loading the game… If it does not start, the full region guide below still works.
How to play. Press Start. Select a region (click a column, or ←/→) and bet H (holds, rigid) or S (smears, mobile). Press R to reveal — the mobile regions jitter — and score. Press Enter or Next.
Why the smeared tail matters
Ubiquitin's C-terminal tail, residues 71–76 ending in two glycines, stays mobile, and that flexibility lets its final glycine be joined to a lysine on a target protein, the tag that sends many proteins to the proteasome.
A snapshot of something that jiggles
A structure — even a crisp space-filling one — is a snapshot or an average of a molecule in constant thermal motion. An NMR ensemble shows this directly: it is a bundle of models, and where they disagree, that region is mobile; where they overlap, it is rigid. (Crystallographic B-factors tell the same story.) So a space-filling picture is not a bag of fixed marbles — that is the misconception this game targets. Ubiquitin’s little C-terminal tail smears; BPTI’s disulfide-stapled core barely moves, though its very ends fray.
Every region in the game is 4 residues long, so its size tells you nothing. Its call comes from the real ensemble: a region smears when its atoms spread at least 1.5 Å across the models (the mean Cα RMSF, after the protein’s core is held still), and holds when they spread less.
The proteins and how they move
Ubiquitin · UBB · P0CG47 · PDB 1D3Z (NMR ensemble)
| Region | Residues | Spread | Moves? |
|---|---|---|---|
| Start of the N-terminal β-hairpin | 1–4 | 0.08 Å | Holds (rigid) |
| Inside the core (helix + β-sheet) | 24–27 | 0.09 Å | Holds (rigid) |
| Inside the core (helix + β-sheet) | 44–47 | 0.09 Å | Holds (rigid) |
| C-terminal tail (…LRGG) | 73–76 | 3.25 Å | Smears (mobile) |
Measured with the core (residues 18–70) held still.
BPTI (trypsin inhibitor) · BPTI · P00974 · PDB 1PIT (NMR; mature-chain numbering — UniProt residue = mature + 35)
| Region | Residues | Spread | Moves? |
|---|---|---|---|
| N-terminal end | 1–4 | 0.73 Å | Holds (rigid) |
| Disulfide-stapled core | 20–23 | 0.23 Å | Holds (rigid) |
| Disulfide-stapled core | 41–44 | 0.35 Å | Holds (rigid) |
| C-terminal end | 55–58 | 2.13 Å | Smears (mobile) |
Measured with the disulfide-stapled core (residues 5–55) held still.
Calmodulin · CALM1 · P0DP23 · PDB 2K0E (NMR, 160 models; chain numbering — UniProt residue = chain + 1)
| Region | Residues | Spread | Moves? |
|---|---|---|---|
| N-terminal end | 1–4 | 4.05 Å | Smears (mobile) |
| N-lobe (EF-hands 1–2) | 26–29 | 0.59 Å | Holds (rigid) |
| Central linker | 77–80 | 5.25 Å | Smears (mobile) |
| C-lobe (EF-hands 3–4) | 97–100 | 18.61 Å | Smears (mobile) |
Measured with the N-lobe (residues 5–68) held still.
Methods & about
This is a teaching game and honest about being a simplification: the sphere cluster is a schematic space-filling view (not real atomic coordinates), and “holds vs smears” is a coarse, binary stand-in for continuous per-residue mobility. The calls are measured, not written: for each protein we take its NMR ensemble from the PDB, hold its core still, and compute how far each Cα spreads about the mean (RMSF); a region at or above 1.5 Å smears. An NMR ensemble is a set of models that all fit the measurements, not a film of one molecule; where they disagree, the protein moves. The jitter is undirected thermal wobble — atoms bump and jiggle, they do not travel with purpose. The examples are canonical: ubiquitin (rigid core, mobile Gly-Gly tail), BPTI (a textbook rigid, disulfide-locked protein), and calmodulin (rigid lobes on a flexible central linker). The region names and notes are written by hand and science-checked; every number and call is computed. No accounts, no storage, no servers.
Want to see real structures in 3D? Open the free AlphaFold viewer. Everything we make is free and non-profit; learn more on the home page.