Hi Bob, The mapped surfaces require a second cube file. The most common situation is where the electrostatic potential (ESP) is mapped onto the total electron density surface. The electron density surface is constructed as you described, and once the grid points defining the surface have been determined they are used to determine the value of the ESP from the second cube. The ESP value then determines the color at that point of the surface.
A slice through a cube would have one value defined by the user (i.e. a slice at X=0). The surface could then be color coded by the value of the grid point from the cube file. Rick <What the JVXL format does is: (a) identify all points in the stream of data where we cross the surface, thus identifying all (.) and (o), and then (b) identify the fractional distance from one end of each critical edges to the other (where the "x" goes) and encodes that as an ASCII character between 35 and 125. These are the only two pieces of information required to draw a monochromatic surface with 99% precision in relation to the position of the surface within each voxel. For colored surfaces, we also need a color index at each surface point (x). This could be from the original data or it could be from mapping a separate set of voxel or functional data onto it. I hope to add that soon. It will be a set of ASCII characters again, because the "rainbow" of colors is really just 36 distinct color values. It will be the same length as the edge fractional distance string. But first I need to understand how one maps information like this onto a set of voxels or surface points. Bob -- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein > ------------------------------------------------------- All the advantages of Linux Managed Hosting--Without the Cost and Risk! Fully trained technicians. The highest number of Red Hat certifications in the hosting industry. Fanatical Support. Click to learn more http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
