------------ CCP4 Newsletter - January 1997 ------------

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Interactive Visualization of Macromolecular Crystal Packing with Internet Tools: VRML and Java

Yu Wai Chen and Tai Y. Fu

Information interchange has been totally revolutionized by the recent developments of internet-relating software standards. Among these, two of the hottest areas that are of particular interest for interactive visualization of 3-D models are the Virtual Reality Modeling Language (VRML) and the Java language. VRML is an emerging standard for describing non-static navigatable 3-D environments and is particularly useful for sharing 3-D models over the internet. Java is an object-oriented language that allows generation of machine-independent programs to be executed from WWW browsers. With Java, 3-D models can be described with objects like lines and spheres.

To exploit the use of these tools in visualizing intermolecular interaction of macromolecules, the authors have developed WWW services which transforms Brookhaven PDB coordinate files into 3-D crystal packing models that can be manipulated interactively. VRML 3-D world files can be examined with an external VRML browser (e.g. Webspace from Silicon Graphics) or a VRML viewer plugin (e.g. CosmoPlayer from SGI) for the WWW browser. A 3-D model created with the Java applet can be displayed and manipulated in a Java-enabled WWW browser (e.g. Netscape 3.0) directly. The VRML method has been described in full in Fu & Chen (1996).

VRML service, "xpack": http://dta.med.harvard.edu/ubc/banff/xpack.html
Java service, "Java lattice": http://dta.med.harvard.edu/ubc/kelowna/latte.html

The user interfaces of both services are very simple; users are just required to fill out a form specifying only two parameters:

The core of both Web services consists of a "translator" program that converts a PDB file into the respective 3-D models. In the case of the VRML service, this is achieved with a Common Gateway Interface (CGI) script written in the Perl language. The PDB file submitted by a user is translated in the remote server machine into a VRML world file which is then returned to the user's local machine for display. The user can also choose to install the service on their local machine if they plan to use the service frequently. For the Java service, the "applet" contains all programming instructions required for coordinates translation and model display. Coordinate translation is done in the user's local machine.

The algorithm of the two translator programs are similar:

Unit-cell parameters and space group information are first extracted from the 'CRYST1' record of the PDB file. If this record is missing, only the identity molecule will be displayed in the output model. The translators do not read the 'SCALEn' lines and do not support non-standard orthogonalization of coordinates. The symmetry operation data used are extracted from the library file, symop.lib from the CCP4 suite.

Speed is the major concern with any 3-D rendering. The manipulation of complex models requires extensive computing resources and can be painfully slow. Hence, in designing the Web services, the aim is to make the simplest 3-D model (wireframe) which allows the fastest response to the client and, at the same time, contains adequate molecular information for packing analyses. Consequently, the simpler approach of drawing all atoms and determining their connectivities by summing their covalent radii was abandoned. Instead, only the most interesting features of the macromolecule(s) are presented to achieve maximum computing performance. At present, these features include the protein alpha-carbon (C-alpha) backbone, disulphide bridges, haem groups, and the phosphate backbone of nucleic acids. The resulting 3-D model consists of the crystallographic unit cell and the macromolecules in various symmetry-related positions. In the Java service, the user can also choose to display in the all-atom mode.

Both of these 2 methods are potential tools for further development in the visualization of 3-D scenes. We can envision that machines with ever-increasing CPU speed and memory will one day allow photo-realistic model rendering with surface polygons (rather than lines) to be used in this kind of applications.


Fu, T.Y. and Chen, Y.W. (1996). Visualization of macromolecular crystal packing using Virtual Reality Modelling Language (VRML). Journal of Applied Crystallography, 29, 594-597.

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