Molecular World Navigation

Final Reports

• Somrat Niyogi : Primary and Secondary Structures Generation
• Dave Harding : Dynamics for Molecular Animation, another report
• Sadia Malik : Inverse Kinematics For Molecular World
• Russell Gayle: Creating multiple Levels of Detail for Molecular surfaces
• Bong-Soo Sohn: Adaptive LOD Isocontouring
• Matt Anderson : Multi-Tiled Displays
• Ben Kirk : Browser Support

Useful Links

• Representation of Molecular Models and Rendering Techniques
• Protein Data Bank
• Molecular Dynamics Movie (Wyatt Research Group, Movies,Image/Movie Gallery)
• Molecules Viewer and Geometry Output Generation
  • PyMol
  • MolScript
  • SGI Performer libraries/Perfly Application for linux
• VMD - Visual Molecular Dynamics
• Wadsworth Center
• PDB Molecule of the Month for April Anthrax Toxin

Steps

1. Building Static Objects

2. Building a Scene + Guidemap

3. Building Dynamic Objects

4. Fast Interactive Browsing + Use of Guidemap for Controlled Tour

5. Multi-Tiled Display

Progress

• Building Static Objects
  • Secondary Structures of 6 molecules generated
  • Primary Structures of 6 molecules generated - Yufeng/Shubing
  • Gave a presentation in class about secondary structure algorithm and the basics of structures

  Molecules with primary and secondary structure generation and display(HIV1,RNAP,1A02,gramicidin), PDB data are provided by Protein Data Bank. Images are rendered by MolScript.

  
• Fast Interactive Browsing (Multiresolution Model Generation)
  Simplified Models were created by Mike Garland's Qslim program.
  
  • Multiresolution representation of 1a02 molecular surfaces from electrostatic potentials
    
    Original (face#:132440(red)+161784(blue)), Simplified 1 (face#:5000(red)+5000(red)), Simplified 2 (face#:20000(red)+20000(red))
    
  • Multiresolution representation of 1a9u molecular surfaces from electrostatic potentials
    Original (face#:186296(red)+171524(blue)), Simplified 1 (face#:5000(red)+5000(red)), Simplified 2 (face#:20000(red)+20000(red))
• Building Dynamic Objects.
  Isosurfaces from Time-Varying Electronic Density maps of Alanin Molecules (timestep 0,2,4)
  molecular dynamics simulation is done by NAMD .
  A sequence of PDB files are generated by VMD .
  Electronic density map of Each PDB file can be generated by Dr.Zhang's program.
  Isosurface of each electronic density map is constructed by ContourIV.
  
• Multi-Tiled Display with Chromium by Matt Anderson.
  

1. Building Static Objects

Participants : Shubing Wang, Yufeng Zhang, Somart Niyogi

        (1) CPK

        (2) Solvent Accessible Surface

        (3) Solvent Excluded Surface

    (4) Isocontour of Electrostatic Potentials ( Dataset )

Papers

X. Zhang, C. Bajaj, W. Blanke
Scalable Isosurface Visualization of Massive Datasets on COTS-Cluster
Proc. of IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics, pg. 51-58, San Diego, CA, 2001 (pdf)

C. Bajaj, H.Y. Lee, R. Merkert, V. Pascucci
NURBS based B-rep Models from Macromolecules and their Properties,
In Proceedings Fourth Symposium on Solid Modeling and Applications, Atlanta,Georgia, 1997,C. Hoffmann and W. Bronsvort Eds., ACM Press. pp. 217-228 (ps.gz)