A Crystallographer's Guide to Internet Tools and Resources

VRML - Virtual Reality Modeling Language

VRML is to 3D graphics what HTML is to text: it is a common format that can be displayed on any computer using a standard WWW browser (For instance Netscape or Explorerequipped with a viewer, see the VRML repository) or using a standalone viewer.

It allows the user to click on links to other objects (hypertext mark-up). As a trivial example, the following file displays two spheres in 3D, with the address of another VRML object (bcc.wrl) anchored to the first sphere.

#VRML V1.0 ascii
WWWAnchor{name "http://www.ill.fr/dif/vrml/bcc.wrl" Sphere{}}
Translation {translation 1 1 1 } Sphere {}

Complex 3D crystal structures can be described in VRML, including space filling, ball-and-stick, co-ordination polyhedrae etc.. They can be explored from the inside with full interactivity. The translation of three dimensional crystallographic objects into VRML is facilitated by way of converters able to change a conventional set of coordinates into a standard .wrl file. There is no need to speak VRML like a specialist.

VRML Authoring for Crystallographers: The tool market is growing with either downloadable converters such as pdb2vrml, xtal-3d, CRYSTAL, MOLDA and STRUVIR or online builders (send your data and receive the corresponding .wrl file in return) such as Builder 1.2 for membranes, PDB to VRML, the Crystal Packing Visualization by VRML system (Tai Y. Fu and Yu Wai Chen, J. Appl. Cryst. 1996, 29, 594-597), the Chemical VRML Generation Service and xtal-3d which is able to access to the Inorganic Crystal Structure Database.

Example VRML Files: A non-exhaustive list includes Chemical Examples, 3D Scenarios of Biomolecules, Silicates (aluminosilicates and zeolites announced), the ILL's Gallery, an Introduction to Crystal Structures, the JICST Crystal Structure Database, 6-connected 3D nets, the IUMSC Database, Biological Macromolecules.... Some of them were built using the above converters.

General Documentation: It is recommended to read the FAQ, to visit the VRML repository and its list of Browsers, to subscribe to the VRML Forum, to respect the VRML versions 1.0 and 2.0 specifications, to consider the SGI site and the Yahoo selection, to read and post messages to the comp.lang.vrml Newsgroup.

Conclusion: As a general tool for 3D visualization in crystallography VRML was unexpected. The real usefulness of current or future possibilities like 3D mark-up, multi-user connections, links to sound or other media is an open question. Not everything that uses VRML will necessarily be an Internet application. Producers of drawing programs for crystallography should consider at least offering a .wrl output file option to their users. Availability of free PC converters should boost VRML applications in crystallography. Finally, without the possibility to save high quality 2D projections of a selected 3D view and to print them, crystallographers at large might not adopt the baby. At the moment quality depends on your maximum screen resolution.

What is New since IUCr XVII ?

The conference VRML as a tool for exploring complex structures given at the IUCr XVII Congress (Seattle, USA, August 8-17, 1996) is online (abstract, full text, transparencies and VRML example files).
The demo of the latest version of Crystallographica including a VRML export function is available.
Plot your 3D-diffraction scans at ILL by Surf3d.
Download the free MSI WebLab Viewer and test its VRML export function.
Tessel is a molecular modeller with POVRay and VRML output, generates parametric surfaces, produces several forms of sphere tesselations.
"Kittel, Chapter 1" as virtual reality world available.
A new graphical routine, VRSTPLOT, has been added to GSAS (Rietveld software). It produces very spiffy 3D graphics via the VRML 1.0 format (structures and also Fourier contours).
Viseur is a program that lets you manage and visualize your preferred GPCRs (G Protein-Coupled Receptors). Based on an alignment and a template protein (PDB file) one can build a 3D model and view it (change it in the future) with OpenInventor viewers or a VRML viewer by using the ivToVRML translator.
A virtual chemistry lab at the University of Oxford.
GLASSVIR prepares VRML files for 3D visualization of RMCA glass modelling results.
DRAWxtl is a program to display crystal structures for dissemination across the net using VRML and for publication using the POV-RAY scene language (or screen copy). It can read CIF, CSD, GSAS, SCHAKAL and SHELX formats as well as its own native format.
VMD (Visual Molecular Dynamics) can write to various 3D file formats including VRML.
WebMolecules proposes 2000 3D models in VRML-2. Most of these are organic, but there is a crystal category which contains about 14 models. In addition, this is the home site for Molecular Arts Corp., producers of Molecule-3D and other commercial software.
X-STEP, the X-ray structure evaluation package from STOE can save VRML models.
A Review on Virtual Reality in Chemistry is available (J.Mol.Model. 1997, 3, 386 - 402), discussion is open.
MolMol is a nice tool for visualization of proteins and can make VRML plot. There are binaries for SGI, DEC, Linux ... and Win95!
Molscript V 2.0 is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations. One of the output modes is in VRML 2.0. The MolScript program has been completely rewritten in the C programming language. The MolScript C source code is strict ANSI C, and should therefore compile with any ANSI-C compliant compiler.
The Internet Journal of Chemistry explains how creating enhanced Web pages, including creating VRML pages.
Cosmo Player 2.0 has recovered the Live 3d quality with VRML 2.0. A VRML1 to VRML2 translator allows to reuse your previous work. Nevertheless, a Pentium II with sufficient memory is better.
DIAMOND 2.0 - Visual Crystal Structure Information System. A free-of-charge trial version is available for download. Saving in VRML 1.0 is even possible with the demo version.
VRML File Creator for Chemical Structures.
The Java Structure Viewer (JSV) from Steffen Weber supports Postscript output or direct printing as well as VRML, GIF and JPG outputs.
STRUPLO for Windows is a MS-Windows version of STRUVIR, a program for producing polyhedra plots for

ChemVis : Chemical Visualization on the Internet. Embedded dynamic and interactive high-end graphics in digital documents for the visualization of complex factual relationships. Many VRML compatible tools.