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Survey of the computer visualization environment at the IMV

Scientific Visualization of Virus Structures

Platforms used at the IMV

Programs used at the IMV

Other powerful packages

  • Stanford based Molecular Applications Group MacImdad(R) program. Info to obtain a demo by ftp is availabe here.

The data

Two types of data are visualized: x-ray crystallographic coordinates and computer-averaged image reconstructions of cryo-electron microscopy photographs. The former provides the highest resolution, usually between 2 to 8 Angstroms, while cryoEM data is usually around 35 Angstroms.

X-ray Crystallographic Coordinates

Atomic coordinates of a virus are collected by x-ray crystallography and then visualized in various ways, such as molecular surfaces, ball-and-stick or space-filling atomic models, and ribbon diagrams. For visualizing a virus, a molecular surface representation is preferable, as it gives an overall view of the solvent-accessible surfaces. Unfortunately, calculation of molecular surfaces is memory intensive and requires sophisticated programs like Grasp for the SGI. Plotting of the atomic coordinates provides details such as interactions between amino acid residues, but this detail becomes clutter when visualizing an entire virus, which contains dozens of proteins. One can circumvent this problem in either of two ways: plot a molecular surface (preferable) or simplify the atomic plot to include only the alpha-carbon backbone of the molecule (i.e. c-alpha trace), leaving out the amino acid residues (A c-alpha trace is better when computing power is limited). Atoms are usually represented as ball-and-stick or space-filling (Van der Waals surfaces). Midas, O or Sybyl on the SGI or MolView, MacMolecule, or Kinemage on the Mac are excellent programs for this type of visualization. Although not useful for visualizing the entire virus, ribbon diagrams display nicely a protein's secondary structure (e.g. alpha-helices and beta-strands) and can be produced by Ribbons on the SGI or MolView for the Mac. An example ribbon diagram made with MolView shows the VP1 protein of rhinovirus 14 with the WIN drug bound.

Some examples can be found on the Visualizations of Virus Crystal Structures page.

Cryo-electron microscopy and image reconstruction

The data is in the form of three dimensional scalar lattices, meaning that each node (location in 3-D space) is associated with a scalar density value. We visualize the datasets using Explorer 2.2 on the SGI (Nice description of Explorer at NCSA Pathfinder Project). We may also start using Data Explorer, which would also be run on the SGI (I know of no analogous program for the Mac). The structure of the virus can be presented as a 3-D isosurface (a plot of all the nodes with a data variable equal to a chosen threshold value), a collection of volume elements or voxels (3-D volumetric rendering), or 2-D slices of a 3-D scalar field. I'm in the process of implementing volume rendering with Explorer of the datasets, as it will allow visualization of gradations in density in the virus particle.

Some examples can be found on the 3D CryoEM Reconstructions page.

(Other examples of 3D Image Reconstructions)

Be sure to check out the Scientific Visualization and Graphics page at the University of Minnesota.

Go to the Web Server for Virology home page

Content: ©1994-1997 Stephan Spencer & Jean-Yves Sgro
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Last Modified October 23, 1998