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
3/4 or Explorer 3/4
equipped with a viewer like Live3D,
the SGI Cosmo Player
or the Microsoft VRML
Add-In...) or a standalone viewer (VRweb...).
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.
- "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.
[Index]
- 16th September 1997 - © Alan Hewat
and Armel Le Bail - Not
to be copied or reproduced without permission - Authors' current manuscript
