This example shows a density map as a partially transparent solid in Chimera. High density values are brightest and most opaque. Rendering as a solid uses the complete data volume providing more information than an isosurface, particularly when the view is rotated. The example shows how Chimera is used to examine the agreement between data and a model derived from the data.
|Figure 1: Ribbon diagram of bluetongue virus VP7 monomer. Matthew Baker and Wen Jiang of the National Center for Macromolecular Imaging simulated an 8 angstrom resolution density map based on this crystal structure (chain 1 of RCSB entry 1bvp). They used the simulated data to test their programs Helixhunter and Foldhunter which find alpha helices and folds in density maps. The programs are described in a Journal of Molecular Biology article.||Figure 2: Simulated 1BVP density map and blue rods representing where helices are found by the Helixhunter program. The blue rods have 1 angstrom diameter. chosen smaller than the the diameter of an alpha helix so the density map is not hidden. The 9 helices are well resolved in the 8 angstrom simulated density map. Helixhunter finds them but does not always realize their full length as shown in figures 3 and 4. QuickTime movie (1.9 Mb) of data and helixhunter cylinders being rotated.|
|Figure 3: Predicted helices in blue at the top and bottom left are shorter than the density map sausages they model.||Figure 4: Different view angle puts the poor fitting helices at the upper right and lower right. The density map sausage for the upper right helix is seen to be curved. The blue rod for the lower right helix is not aligned parallel to its sausage.|
The images were produced using the Chimera molecular visualization program developed by the Computer Graphics Lab at UC San Francisco. The model and data can be interactively rotated, and scaled, and thresholds adjusted using the mouse. The images were captured on an SGI and are best viewed on a SGI or Mac. They will look dark on a PC, Sun, or DEC Alpha because those platforms don't do gamma correction.
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