Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four
independent modes: an HTML5-only web application utilizing jQuery, a Java
applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side
component (JmolData.jar). Jmol can read many file types, including PDB, CIF,
SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian,
GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other
quantum chemistry programs. Files can be transferred directly from several
databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple
files can be loaded and compared. A rich scripting language and a well-developed
web API allow easy customization of the user interface. Features include
interactive animation and linear morphing. Jmol interfaces well with JSpecView
for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD
programs for 3D printing (VRML export).

See also: https://sourceforge.net/projects/jmol/