“Web-Based Molecular Visualization Using Procedural Shaders in X3D” by Liu, Owen, Zhu, Weber and Harrison
Conference:
Type(s):
Title:
- Web-Based Molecular Visualization Using Procedural Shaders in X3D
Session/Category Title: Technical Track
Presenter(s)/Author(s):
Moderator(s):
Abstract:
The introduction of programmable graphics processing units (GPUs) and the addition of procedural shaders to the web3D standard X3D provide new techniques to develop real-time web-based visualization. This paper discusses the applications of these techniques to bioinformatics and chemistry visualization, specifically the visualization of large biomolecules. By using procedural shaders, we are able to produce higher quality visualizations with minimal performance penalty. We have developed methods to automatically convert from the standard bioinformatics PDB format to CML and then to X3D. The procedural shaders are automatically inserted during the CML-to-X3D conversion. This provides higher quality images and leads to future possibilities of more flexible and enhanced visualizations.
References:
[1]
Badger, J.: An evaluation of automated model-building procedures for protein crystallography. Acta Crystallographica. International Union of Crystallography pp. 823–827. (2003)
[2]
Bernstein, H. J. and Sayle, R: RasMol Molecular Graphics Visualization Tool. (2000): www.openrasmol.com
[3]
Bitmanagement (2005): www.bitmanagement.de
[4]
Blinn, J. F.: Models of Light Reflection for Computer Synthesized Pictures. Computer Graphics, Vol. 11, No. 2, pp. 192–198, July 1977 (Proceedings of SIGGRAPH 77).
[5]
Blinn, J. F.: a Generalization of Algebraic Surface Drawing. ACM Transactions on Graphics, 1:3, pp. 235–256. (1982)
[6]
Casher O., Leach C., Page, C. S. and Rzepa, H. S., Virtual Reality Modelling Language (VRML) in Chemistry. Chemistry in Britain, 34, 26 (1998)
[7]
Chem Vis Group on Chemistry Visualization. (2005)
[8]
www2.chemie.uni-erlangen.de/projects/ChemVis/index.html
[9]
www.ccc.uni-erlangen.de/
[10]
wwwvis.informatik.uni-stuttgart.de/
[11]
Chemical Markup Language (2005): www.xml-cml.org
[12]
De Carvalho G. N. M.: High-level procedural shading VRML/X3D, Proceedings of the SIGGRAPH 2003 conference on Web graphics: in conjunction with the 30th annual conference on Computer graphics and interactive techniques, San Diego, California (2003)
[13]
De Carvalho, G. N. M., and Gill, T., Parisi, T.: X3D Programmable Shaders Proceedings of the ninth international conference on 3D Web technology 2004: pp. 99–108 (2004)
[14]
Fernando, R., and Kilgard, M. J.: The Cg Tutorial: The Definitive Guide to Programmable Real-Time Graphics. Addison-Wesley (2003)
[15]
Gouraud, H.: Continuous Shading of Curved Surfaces. IEEE Transactions on Computers Vol. C-20, No. 6 pp. 623–629, June 1971.
[16]
Google hits for various Web3D technologies: (2004): www.macWeb3D.org/ewiki/index.php?id=most%20popular% 20 Web3D%20format
[17]
Krieger, J. H.: Doing Chemistry in a virtual world: VRML, a new web technology, holds promise for chemistry in three dimensions American Chemical Society (1996)
[18]
Lindholm, E., Kilgard, M. J., and Moreton, H.: A User-Programmable Vertex Engine. Proceedings of the 28th annual conference on Computer graphics and interactive techniques, pp 149–158. (2001)
[19]
Liu, P., Wang, Y. F., Ewis, H. E., Abdelal, A. T., Lu, C. D., Harrison, R. W., and Weber, I. T.: Covalent Reaction Intermediate Revealed in Crystal Structure of the Geobacillus Stearothermophilus Carboxylesterase Est30. Journal of Molecular Biology, pp. 342–551 (2004)
[20]
Mark, W. R, Glanville, R. S., Akeley, K., and M. J. Kilgard: Cg: a system for programming graphics hardware in a C-like language. ACM Transactions on Graphics 22(3), pp. 896–907. ACM Press, July (2003)
[21]
Ngan, A., Durand F., Matusik, W.: Experimental Validation of Analytical BRDF Models. Sketch of SIGGRAPH2004 July (2004)
[22]
PDB: Protein Data Bank Resource. (2005): www.rcsb.org/pdb/
[23]
Peeper, C. and Mitchell, J. L.: Introduction to the DirectX? 9 High Level Shading Language (2002): www.ati.com/developer/ShaderX2_Introduction To HLSL.pdf
[24]
Phong, B. T.: Illumination for Computer Generated Pictures, Communications of the ACM, Vol. 18, No. 6, pp. 311–317, June 1975.
[25]
Perrakis A., Morris R., and Lamzin V. S.: Automated protein model building combined with iterative structure refinement. Nature Struct. Biol., pp 458–463 (1999)
[26]
Ploys, N.: Stylesheet Transformations for Interactive Visualization: Towards Web3D Chemistry Curricula. Proceeding of the eighth international conference on 3D Web technology pp. 85–91 (2003): www.3dez.net/X3D/CML/
[27]
Parisi, T.,: Flux: lightweight, standards-based Web graphics in XML, Proceedings of the SIGGRAPH 2003 conference on Web graphics: in conjunction with the 30th annual conference on Computer graphics and interactive techniques. San Diego, California (2003)
[28]
Purcell, T. J., Buck, L., Mark, W. R., and Hanrahan, P.: Ray Tracing on Programmable Graphics Hardware A CM Transactions on Graphics 21: 3, pp 703–712 (2002).
[29]
Rost. R. J. And Licea-Kane B.: The OpenGL(R) Shading Language. Addison-Wesley (2004)
[30]
Raster3D: www.bmsc.washington.edu/raster3d/raster3d.html
[31]
Schroder, H. K., Willassen, N. P., and Smalas, A. O.: Structure of a non-psychrophilic trypsin from a cold-adapted fish species. Acta Crystallogr D Biol Crystallogr 54 pp. 780 (1998)
[32]
Tie, Y., Boross, P. I., Wang, Y. F., Gaddis, L., Hussain, A. K., Leshchenko, S., Ghosh, A. K., Louis, J. M., Harrison, R. W., and Weber, I. T.: High Resolution Crystal Structures of HIV-1 Protease with a Potent Non-Peptide Inhibitor (Uic-94017) Active Against Multi-Drug-Resistant Clinical Strains. Journal of Molecular Biology. pp.338–341 (2004)
[33]
Web3D-ToolKits: X3D Toolkits CD SIGGRAPH2003. (2003)
[34]
Web3D Consortium. (2005): www.Web3D.org
[35]
Web3D-Shader-Group (2005): www.web3d.org/x3d/workgroups/x3d-shaders.html
[36]
Web3D-Tools (2005): www.web3d.org/applications/tools/viewers_and_browsers/
[37]
Zou, Y.: Built VRML model of 3D molecular structures (1999): www.molvrmltripod.com
[38]
Zara, S.: PDB2CML Implementation (1999): www.xml-cml.org/software/pdb2cml.html
