On 6/30/2010 2:33 PM, Jeff Hansen wrote: > Glad that helped. Making it easily accessible to students means doing > most of the work for them. In the case of Jmol that means setting up > buttons or checkboxes or whatever user interface then scripting what > you want the students to see. In the case of viewing the MOs or some > other surface you could create a button which the students would click > to show the surface. Would be easy enough to include in that script a > command to return to model 1 so the MOs would be available to view. > > Those surfaces in Spartan are basically the electron density surface > colored according to other properties. Jmol will certainly allow you > to visualize the electron density surface. My understanding is that > you can also color it by whatever property you want. There would be > some serious scripting involved in doing this. Without knowing > exactly what is in the smol file, I would imagine the data for those > properties are there somewhere. you would have to grab that data > somehow then instruct Jmol to use it as the basis for coloring the > surface. I'm no expert on this, but perhaps someone else can help > with the details of this. > > Thanks for your suggestions. More or less that was my plan as far as buttons are concerned. I am trying to sort out what kind of files do I want to use as Jmol input, and what is the easiest way to set things up. I am at the exploratory stage (new to Jmol) so I running into occasional "glitches" as the one with vibrations/surface data.
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