3Dmol.js vs ChemDoodle Web vs Mol* — same file, same style, side by side

Structure Style Colour Orientation Shading

3Dmol.js

ChemDoodle Web

Mol*

What to look at:

Load time in each header — same bytes, parsed three times. Mol*'s first number includes ~300 ms of one-time plugin boot; every later change is cheaper.
Cartoon quality. 3Dmol draws proper secondary-structure cartoons (arrows on strands, tubes on loops); ChemDoodle draws a ribbon; Mol* draws the most refined of the three. Compare on 1IGT, which is nearly all β-sheet — the arrowheads and the strand twist are what to watch.
Molecular surface. 3Dmol and Mol* both compute one (SES/SAS); ChemDoodle Web has no surface at all — pick "Molecular surface" and read the middle note. On 2HHB, 3Dmol took 5.7 s and Mol* 9.4 s, but Mol* builds on a worker and stays responsive while it does. This is the one capability our own renderer also lacks — see the gaps list in docs/bio-rendering-thorough.md.
Big structures. 1AON is the honest test of whether either can carry a lesson on a school Chromebook.
Ligands. 3CYT's heme and 1ATN's ATP — do they survive the cartoon representation, and are they coloured usefully? 2HHB has four haems, one per subunit, so it asks the same question four times over.
Colour schemes, on 2HHB. The default structure, and the one to cycle the Colour menu on. Four chains make "by chain" meaningful; being all-α makes a secondary-structure scheme a clean two-colour test (helix vs loop) instead of three colours fighting; and the four haems show whether a scheme reaches HETATM at all or quietly leaves them to a fallback. Note that ChemDoodle's chain colours are its own and cannot be overridden — that finding is why protein-lab.html reads them back out of the molecule instead of setting them.
Licence. 3Dmol.js is BSD-3, Mol* is MIT, ChemDoodle Web is GPLv3 (or paid commercial) — GPL means the page loading it inherits GPL terms. Settled: ChemDoodle is dropped for exactly this reason, and neither permissive alternative was adopted either — see RenderingLibraries.md.
Why three panes, given we adopted none of them. The decision was structural, not aesthetic: every viewer here brings its own WebGL context and camera, so none can draw into scene.js's scene alongside our FX, raycasting and shared zoom ladder. What survives is this page as a style reference — when we build a representation ourselves, these three are the convention to measure it against. Read the Style menu as a spec, not as a shortlist.