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Interactive Visualization of Complex Molecular Ribbon Structures

This presentation explores advancements in visualizing complex molecular ribbon structures, presenting an overview of ribbon structures, existing tools, and proposed improvements. Existing software like RasMol, Chimera, and PyMol have limitations in rendering with dynamic transitions between secondary structures. We introduce combined boundary representations (BReps) for enhanced visualization, utilizing a multi-resolution approach and B-spline curves to produce smooth, interactive models. A live demonstration highlights the effectiveness of these techniques, developed through collaboration between TU Braunschweig and GBF.

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Interactive Visualization of Complex Molecular Ribbon Structures

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  1. 8th International Conference Information Visualisation 2004 “Visualization of Complex Molecular Ribbon Structures at Interactive Rates” Andreas Halm, Lars Offen, Dieter Fellner (TU Braunschweig)

  2. Overview • What are ribbon structures? • Existing tools • Improvements • Representation based on Combined BReps • Dynamic Tessellation • Live Demo

  3. Credit Ribbon Visualization results from the collaboration project BioBrowser (funded by the German Research Foundation, DFG) between the • Institute of Computer Graphics, TU Braunschweig and • Structural Biology,Ges. f. Biotechnologische Forschung (GBF), D. Heinz, G. Dieterich, J. Reichelt

  4. Ribbon Structures • Schematic drawing of the backbone • Secondary Structure • -Helices • -Strands • Random turns • Tertiary Structure • Folding • -Sheets

  5. Existing Tools – RasMol • Not passing through C-positions • Static, low Quality • No transition between different secondary structure types

  6. Existing Tools – Chimera • Not passing through C-positions • Moves C-positions to match ribbons • Static Quality

  7. Existing Tools – PyMol • Passing through C-positions • Static Quality • No transition between different secondary structures types

  8. Improvements • Ribbons pass through C-positions • Using multi-resolution approach • Continuous transition between different secondary structure types

  9. smooth face sharp face crease edge Combined BReps • Combination of • polygonal Boundary Representation • Catmull/Clark Subdivision Surfaces • Sharpness flag for each edge

  10. Combined BReps • Subdivision level is controlled by • View frustum clipping – • Frame rate – • Projected size + • Curvature + • Contribution to the silhouette +

  11. Spline Interpolation • Underlying structure of a ribbon is a B-spline curve • given: C-positions • desired: control points • done by solving a system of linear equations, derived from a decomposition into Bézier segments

  12. Building the Ribbon Structure • The structure of an amino acid determines the quad for each C • Each quad is normal to the tangent of the B-Spline curve in C • To avoid twisted ribbons re-labeling may occur

  13. Building the Ribbon Structure • Base mesh is generated by just joining the quads • Arrows are very easy, too • Using one base mesh smooth transition

  14. Live Demo Demo

  15. References • J.Richardson. The anatomy and taxonomy of protein structure. Adv. Protein Chem.,pages 167-339, 1981. • RasMol: http://www.rasmol.org • Chimera: http://www.cgl.ucsf.edu/chimera/ • PyMol: http://pymol.sourceforge.net/

  16. Thank you for your attention!

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