I guess I'll have to have somebody show me how that works.
If this produces the same result as
http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm? -- I
mean you can click on any point on the graph, and the corresponding
conformation is displayed, that's great. Still, it seems rather involved. Do
you have to enter each dihedral individually into the spreadsheet?
Bob
On Thu, Jul 1, 2010 at 1:22 PM, Jeff Hansen <jhan...@depauw.edu> wrote:
> Bob,
>
> You can do this in Spartan. For example, make a butane molecule and create
> a dihedral angle constraint. Display the properties window and click on the
> dihedral angle constraint to show the properties for it. Set it to vary
> from -180 to 180. Set up an Energy Profile calculation and run it. When it
> is done, close the original butane molecule so only the results of the
> Energy Profile calculation are showing. Select the dihedral angle. At the
> bottom right of the screen, next to where it shows the value of the angle
> should be a letter P in a yellow box. Click on it. It should enter the
> dihedral angle values into the spreadsheet. You can also enter values for
> the energies in whatever units you want or the relative energy (it will set
> the lowest energy to zero). Now go to the Display menu and choose Plots...
> Make sure the Properties checkbox is checked. Choose Constraint from the
> X-axis popup and whatever energy you want from the list for the Y-axis then
> click OK.
>
> This is all in the Mac version. Might be a little different on the Windows
> version. But it definitely will do it and it isn't too hard.
>
>
> Jeff
>
>
> ***********************************************
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***********************************************
>
>
> On Jul 1, 2010, at 12:37 PM, Robert Hanson wrote:
>
> about Spartan --
>
> I guess I'll stick with
> http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm You
> can just drag and drop any Spartan file into that applet, and it will
> display the associated clickable graph. Hopefully they will get a feature
> such as this into some future edition of Spartan Student. For now this will
> have to do. I don't see spreadsheets very appealing unless there is a direct
> clickable interface between their data and the actual conformation. It's the
> connection between the specific energies and the specific conformations that
> my students need to make, not so much the overall energy picture.
>
> Bob
>
> >
>
>> > I have a Spartan question: How do you construct an energy profile plot
>> > that allows you to easily correlate specific conformations to specific
>> > energies (as for example with butane)? I can do that in Sygress/CaCHE
>> > or using Spartan files with my Jmol/Google plot page, but is there
>> > some way of doing that directly in Spartan?
>> >
>> > Bob
>>
>> I am guessing that you would like to have a "clickable" (or otherwise
>> interactive) graph linking (let's say) energy values with specific
>> conformers. I do not know how to do that.
>>
>> Spartan provides a convenient spreadsheet function that allows one to
>> collect energy data as a function of torsional angle and plot them (or
>> even fit the data). A demonstration case is in the Spartan 08 "Tutorial
>> and User Guide" (p. 98).
>>
>> PM
>>
>>
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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