Question 1

How do I load a PDB file from a local server in 3Dmol.js?

Accepted Answer

Use the $3Dmol.download function with the file URL or parse the data directly. The documentation provides examples for embedding PDB files, and you can adapt it for local paths by specifying the correct source.

Question 2

3Dmol.js vs JSmol: which is better for molecular visualization on the web?

Accepted Answer

3Dmol.js is WebGL-based and offers better performance for complex structures with smoother rendering, while JSmol is Java-based and might have broader browser compatibility but slower speeds. For modern web apps, 3Dmol.js is often preferred due to its acceleration.

Question 3

Can I use 3Dmol.js with React or Vue.js?

Accepted Answer

Yes, but integration requires managing DOM elements and lifecycle events manually. There are community examples and potential wrappers, but no official support, so you'll need to handle updates and mounts carefully.

Question 4

How to change the color of specific atoms based on properties?

Accepted Answer

Use the setStyle method with atom property-based selection, as shown in the examples. For instance, you can style atoms by chain or residue type, applying custom colors through JavaScript code.

Question 5

What are the performance limits for large molecules in 3Dmol.js?

Accepted Answer

Performance depends on WebGL capabilities and molecule complexity. While optimized for large structures, molecules with millions of atoms might require simplification or level-of-detail techniques to maintain smooth frame rates.

Question 6

How to export a 3Dmol.js visualization as an image or video?

Accepted Answer

3Dmol.js provides methods to capture the canvas; you can use viewer.render() and then extract image data via toDataURL. For videos, you'd need to script frame captures, as there's no built-in export feature.

3Dmol.js

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