File formats/Surfaces

File Formats

• General information
• Coordinates
• Chemical structure
• Compressed
• Converters
• Images
• Ray Tracing
• Surfaces
• 3D Objects
• Scripting
• Exporting / saving files
• Support for bond orders
• Support for isotopes
• Support for stereochemistry

File Formats for Surfaces

JVXL (Jmol Voxel)

Jmol reads and writes JVXL files.

This format, unique to Jmol, stores isosurface data in a highly compressed format.

Documented at https://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf

XJVXL

An XML-formatted variant of JVXL (used by recent versions of Jmol, post-11.9.7).

Latest Jmol versions implement this format by default when writing some of the newer features, such as discrete contours and the reading of Efvet (triangle-data files). If you use

set testflag4 true

then it writes XML by default for any isosurface.

The new XML format allows for specifying everything that the original JVXL format did, but does it in a much more understandable way and will be the basis for expanded capability.

The basic layout is shown in this example and is just (figuratively -- all this is really XML):

[header stuff]
[volume data]
[isosurfaceSet]
    [isosurface 1]
        [parameters and information]
        [surface data]
        [contour data]
    [isosurface 2]
    ...

Here [surface data] can be any one of a number of definitions of a surface, including edges and color mapping, or of how color is mapped to a plane, or a definition of a set of triangles (not necessarily an "iso"-surface) and how they are to be colored.

The [contour data] there is somewhat new. This allows one to specify a set of lines running along the surface in any way whatsoever, but typically representing contours.

Pmesh

Jmol reads pmesh files for rendering pmesh surfaces, using not the load command, but the isosurface command.

Note: Jmol versions before 11.7 used the pmesh command for loading the pmesh files.

Example files folder and another example file.

Cube (Gaussian)

See Cube under formats for coordinates.

Open DX

Jmol (11.1.18 or later) reads DX files for rendering isosurfaces and color mapping. DX contains three-dimensional scalar data; most frequently, isosurface and color by molecular electrostatic potential (MEP).

(Not to be confused with JCAMP-DX format, used for spectral vibrational data, which can be shown using JSpecView Applet and MDL Chime.)

Open DX files are produced, among others, by APBS (Adaptive Poisson-Boltzmann Solver). APBS exists in standalone and web-server-based versions, and as a plug-in for PyMOL. There is also an APBS web service integrated into Gemstone, which is a front-end GUI that facilitates the access to computational services run at dedicated web servers (follow the Gemstone tutorial).

Technical:

DX, as Cube, defines a three-dimensional grid of points in space. At each point is a number (a "scalar value"). This set of point values is then used by Jmol to define an "isosurface" -- the surface separating points having values greater than a given cutoff from those that have a value less than a certain cutoff. A typical application is molecular orbitals. The phase parameter of the isosurface command allows bicolor rendering: one color for "points greater than x" and another color for "points less than -x".

Jmol can read DX files and re-export them to much smaller JVXL files.

Generally a MEP data set is not used for the isosurface itself. Rather, it is used to map color onto another isosurface, usually some representation of the "molecular surface".

Bottom line is that we can now take molecular electrostatic potential data that were generated in PyMOL (requires the APBS plugin for PyMOL) or in APBS or Gemstone, and use them to color a surface generated in Jmol.

Documentation:

• Jmol interpretation of DX files and re-exporting into much smaller JVXL files
• DX generation of MEP data by APBS
• OpenDX specification and software package

Efvet

Jmol (version 11.7.12 or later, support is preliminar) reads efvet files for rendering isosurfaces and color mapping. Efvet format is an XML file format used in eF-site, a database for molecular surfaces colored by electrostatic potential, that covers the whole PDB.

The efvet file contains geometric information and coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are described together by the surface color: red --> blue colors correspond to negative --> positive electrostatic potentials, and yellow color indicates the surface of the hydrophobic residues.

XPLOR

Jmol (starting versions 11.8.18 and 11.9.20) can read electron density maps in the XPLOR format (CNS/XPLOR, Crystallography & NMR System, Yale Univ.).

CCP4

Jmol (starting versions 11.8.18 and 11.9.20) can read electron density maps in the CCP4 format (MRC/CCP4, Medical Research Council).

Contributors

AngelHerraez, Kmcallenberg