3Dmol.js
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have option of labels that scale with model
currently implement with a fixed font size for maximum readability
SDF rendering might be a good approach for this, as it scales well and looks crisp with 3D transformations. You could use this implementation as a reference.
There's a growing set of modules on npm that would prove useful for text rendering: https://www.npmjs.com/package/text-modules
Or WebGL/GLSL abstractions in general: http://stack.gl/packages/