Jmol Voxel File Format (JVXL)

Jmol 11.0 introduces a revolutionary way of delivering molecular surfaces over the web -- the Jmol Voxel File Format (JVXL). With a compression ratio on the order of 300-600:1 over color-mapped CUBE files, the JVXL format allows delivery of full protein color-mapped solvent-accessible and solvent-excluded surfaces in 30-60 Kb instead of 10-20 Mb, making practical delivery of molecular surfaces available on the web for the first time ever.

The Jmol application can write these surface files to disk. After transferring the JVXL file to a web-site directory, applets at that site can display the surfaces almost instantly. Command line options for the application allow surfaces to be created automatically if desired.

Supported surface types in Jmol 11.1 development versions include:

fixed-atomic-radius surfaces
adjustable-radius van der Waals surfaces
solvent-accessible surfaces
solvent-excluded surfaces
biomolecular cavities

molecular orbitals
molecular electrostatic potential maps

color-contour-mapped planes
arbitrary f(x,y) surfaces
color-contour-mapped arbitrary f(x,y) surfaces

Details relating to the JVXL file format can be found at http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf with numerous illustrated examples at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htm
and http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm

Posted by Bob Hanson 2007-03-23