>rspinney wrote: > >> 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.
> Ah, then we are all set. I have those two files for CH3Cl. That > explains their common point grid. Makes total sense. I do not believe > this has been considered in Jmol. I want to introduce that. All > suggestions for command syntax welcome. The word "map" would be > appropriate here. This function already exists in Jmol (eg. See http://undergrad-ed.chemistry.ohio-state.edu/Carey5th/Ch04/ch4-2-1.html ) where the commands 'isosurface plus 0.0004 "../mapped/ch3oh-density.cub.gz";' + 'isosurface plus color "../mapped/ch3oh-esp.cub.gz";' + First command loads and generates the electron density surface, and the second one maps the ESP onto the density surface. The only problem is the size of these files, even the "small" ones are 200 Kb, and the larger ones up to 2 Mb (when gzipped). This of course produces slow download times especially over dial up. >> >> 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. >> > Yes, this sounds quite reasonable. So you get a colored plane. Please > suggest a command syntax. How about isoslice ? i.e. isoslice [name] [color range] "cube-file-name" > Bob > -- Rick ------------------------------------------------------- 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
