March 21st, 2011
The open source Visual Molecular Dynamics (VMD) system provides now a native exporter in V1.9 for x3d and x3dom. John Stone just announced the new V1.9 which includes the X3D/X3DOM-specific code.
Visual Molecular Dynamics
The release announcement page includes a link to a simple X3DOM example page John Stone (from VMD-team) made with a very small molecule