File formats/3D Objects

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 3D Objects Exported from Jmol

Recent versions of Jmol application and signed applet can export models to several formats that specify three-dimensional objects and can be read by specialized software, either raytracing or 3D-world.

POV-Ray

Jmol can export, with limited features, the current view of a model into POV-Ray format. This can be done from script or from the pop-up menu, but is better controled using the top menu in the Jmol application, which opens a dialog with options. See File formats/Images for more details.

VRML

Jmol can export, with limited features, the model into Virtual Reality Modeling Language, VRML, version 2, also known as VRML97. This can be done from script or from the pop-up menu.

This feature is partially implemented and subject to further development.

• Jmol exports atoms (as spheres), bonds (as cylinders) and isosurfaces (as IndexedFaceSets). Translucency and color are supported.
• The atom size and color, bond thickness and color, are preserved. The orientation and zoom are not always kept.
• Labels, 3D-positioned echo texts and measurement texts are partially supported:
  • text, color, font family and font style supported
  • font size and offset are fixed
  • multi-line not supported (only 1st line is displayed)
  • alignment not supported (always left)
• Ribbons and cartoons are supported (using hermiteLevel 1 automatically if necessary).
• Other features (dots...) are not supported.

The vrml file can then be opened using several programs and browser plugins, and manipulated in 3D using the mouse.

Depending on your VRML viewer or plug-in, you may need to rename the file to a .wrl extension; we are considering making this the default extension.

From Jmol to Blender

Blender is a free, open source, 3D content creation suite, available for all major operating systems under the GNU General Public License.

VRML files created by Jmol can be imported into Blender (v. 2.42 or later) using the VRML97-Import-Script. One dependency you might need is SimpleParse.

Optimizing VRML files

VRML files of medium to large molecules tend to be huge. Some ways to reduce their size:

• Run them through an optimizer program (see refs. below)
• Compress them using the gzip algorithm, and rename to .wrz which is the standard extension and should (hopefully) be recognized by viewers and browsers.

References

• The Annotated VRML 97 Reference, by Rikk Carey and Gavin Bell. Online documentation for the VRML format, including examples.
• A Guide to VRML 2.0 and an Evaluation of VRML Modelling Tools, by Neil Ashdown and Simon Forestiero. Online documentation for the VRML format.
• Chisel (HVRC Edition), a tool to optimize VRML files.

Maya

Jmol can export, with limited features, the current view of a model into Maya ascii format. This can be done from script or from the pop-up menu. Wikipedia info on Maya

References

• Overview of Maya ASCII file format
• A desciption of the Maya Ascii format

OBJ

Jmol (starting v. 11.7.28) can read files in the obj file format. This format is generated by Wavefront, Java3D and PyMOL. The described objects are handled as isosurfaces in Jmol, so they can be saved in more compact JVXL format, if desired, and also can be mapped with other data.

• Description of obj file format at EG-Models.de, an archive of electronic geometry models.
• Description of obj file format at FileFormat.info: www.fileformat.info/format/wavefrontobj/egff.htm
• Description of obj file format at The Graphics File Formats Page by Martin Reddy.
• Export of obj file format from PyMOL (molecular surfaces).

X3D

Extensible 3D Graphics. This is the successor of VRML.

Not yet supported by Jmol.

References

• X3D for Web Authors, by Don Brutzman and Leonard Daly. Examples.

U3D

Universal 3D format. ECMA-363 Standard.

Not yet supported by Jmol.

The most interesting feature of this format is that it can be embedded in pdf files, providing a 3D experience inside this well established standard for publication.

References

• Universal 3D Sample Software project at SourceForge.

A set of libraries to write, read, extend, render and interact with U3D-formatted data, as defined by standard ECMA-363. Intended as starting point for tools and applications to support U3D (exporters, importers, authoring packages and interactive viewers).

• MeshLab project at SourceForge.

MeshLab is the first open source tool to provide direct conversion of 3D meshes into the U3D format. Now you can create pdf with 3D objects with just MeshLab and LaTeX.

• This page holds a demo that generates a 3D model in PDF from the molecule's PubChem CID. It also allows to download the result in PDF, U3D and IDTF formats.

Collada

Collada formats (KMZ/DAE) are Open Source arrangements that have been incorporated into many 3D packages and support textures/surfaces etc. They are a possible XML replacement to VRML.

Not yet supported by Jmol. There is a feature request for this.

We would need:

• A description of how to specify a cylinder (position/translation, orientation/rotation, radius, length) but not using vertexes or meshes.
• A description of how to specify a sphere (position/translation, orientation/rotation, radius) but not using vertexes or meshes.

References

• General information about Collada.
• Format specification (Collada schema).

Contributors

AngelHerraez, Michaelrandolph, NicolasVervelle, Kmcallenberg, Rzepa