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“ Visualization of Complex Molecular Ribbon Structures at Interactive Rates ”

8 th International Conference Information Visualisation 2004. “ Visualization of Complex Molecular Ribbon Structures at Interactive Rates ”. Andreas Halm, Lars Offen, Dieter Fellner (TU Braunschweig). Overview. What are ribbon structures? Existing tools Improvements

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“ Visualization of Complex Molecular Ribbon Structures at Interactive Rates ”

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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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