From: Bob H. <ha...@st...> - 2006-05-25 14:33:57
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Thanks, Rick. I did realize that (finally) last night and was able to tap right into it. THANK YOU, MIGUEL!!! So look at http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm and see if it fits the bill. Notice that each slice is about 6K -- a bit of an improvement, I think. (And if you REALLY want a fair comparison, gzip that!) So far the compression is pretty close to 500:1 in just about all the cases, and you can put as many slices in one file as you want. If you then use that file for the "load" command I still have to figure out a good way to make these JVXL files easily produced. I could do it with a website, but I'd like to make Jmol.jar be able to do that. I'm uncertain about that method of defining planes -- is the {a b c d} notation acceptable? Where: ax + by + cz + d = 0 Or is there a different standard I should be using? isoslice is an idea; I just stuck with the isosurface command, substituting a plane definition for the first file, since that's really what it is -- a specific sort of surface that is going to be mapped. Bob rspinney wrote: >>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 > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers -- -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |