RIVEM

Function of the program :

The program reads in spherical virus electron-density maps and project the densities along defined radial vectors onto a sterographic sphere. The projected density can be represented as contour lines or as gradient of colors. The program can also read atomic coordinates from a PDB and project chosen residues as roadmap onto the same sterographic sphere. The residues can be labeled and colored in various way. The program is still actively developped. If you have any problem of using it. Please contact the author at Chuan (River) Xiao.

Purpose of the program :

Studies of receptor binding to the surface of parvoviruses presented a problem of how to visualize the interaction between the two complex molecular surfaces. The program RIVEM (Radial Interpretation of Viral Electron density Maps) was developed to project an asymmetric receptor density radially onto a unit sphere using spherical coordinates. The stereographic diagram of the projected densities allows a clear visualization of the receptor footprint on the icosahedral virus surface. A spherical "roadmap" function was incorporated into RIVEM so that virus surface residues were projected within the same unit sphere and therefore superimpose onto the projected receptor densities. The program offers a powerful way to visualize and study the correlation between atomic structures and electron density maps in a generic variety of model systems.

Spherical Systems :

Two spherical coordinate systems were defined in the RIVEM program (see figure below) to match the two different standard icosahedral orientations (see figure inset icosahedrons). This allowed users to visualize their results without having to rotate the map or the atomic coordinates before using the program. In system 1, the definitions of the two polar angles are similar to those used in (Rossman and Blow, 1962), which can facilitate the comparison between X-ray crystallography studies and cryo-EM studies, because these definitions were also used in many X-ray crystallography programs such as the general rotation function program GLRF (Tong and Rossmann, 1997). In system 2, the output results are similar to those of the ROADMAP program (Chapman, 1993), in which X axis points north and Y axis is towards the east on the final 2-D diagram.

EXEMPLES

SOFTWARE :

Download RIVEM

BUG REPORT :

If you meet any bugs or problems of the programs, please email xc@purdue.edu.

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