Jmol 13.0 was released Aug 22, 2012. This major release brings to the stable release several very important new features in Jmol developed over the past year.
New features (see http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm\) include:
allowing nonJava options such as ChemDoodle and GLmol
-- JmolData full "headless" operation for server-side processing allowing image-creation, server processing, and remote cross-domain sourcing for the unsigned applet and applet surrogates such as ChemDoodle and GLmol.
-- COMPARE command
-- reading of JCAMP-DX files having structure/spectra assignment data
using ##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview\)
-- Gaussian log reading of Natural Transition Orbitals
-- automatic PNGJ file caching for immensely faster loading of PNGJ files from remote servers
-- write PNGJ files encapsulate all model file data into one PNG file
-- write image 400 400 PNGJ "http://....." POSTs JMOL or IMAGE or structure to a server as application/octet-stream
-- write MOL adds partial charge data as > <JMOL_PARTIAL_CHARGES> in SDF format
-- multiple-scene PNGJ files allowing minimal or full data loading and scripted animations
-- isosurface caching
-- isosurface MOVE [[...matrix4f...]] moves/rotates an isosurface (for the state)
-- MMFF94/UFF minimization and energy calculation
-- show CHEMICAL
-- show NMR
-- MolecularPlayground -- remote status and remote control
-- solid state physics support
-- integration of JSpecView into Jmol, including 2D spectral display and manipulation
-- extended Jmol SMARTS searching
-- PubChem search for name (which can be a CAS number), cid, or SMILES using ":"