When Jmol reads a Spartan smol file, it accesses all vibrations and all molecular orbitals (supposedly!) They should be accessible via the right-click menu (or by clicking the "Jmol" logo").  MOs are under "surfaces"; vibrations are under "model" (at the top).

Each vibration is another "frame" or "model", and generally one of those models has the MOs. For some readers that is the first model, some the second, some the last. It all depends upon the reader. With Spartan, the MOs should be in model 1, and the vibrations should be the models after that.

Makes sure you have issued

vibration on

if you want to see the vibrations or using that menu, Vibration->ON

http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be a good example of this.

Bob

On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak <pm@chem.psu.edu> wrote:
On 6/29/2010 7:20 PM, Robert Hanson wrote:
I'll look into the mep/mo business. Should not be a problem. Just a bug, I think.
Thank you very much for your help.

I do have two related questions:

1. Can more than one surface be read from these files by Jmol?

2. Can Jmol write jvxl files with multiple surfaces?


Since I have just started learning Jmol and have noticed the incredible amount of work you have put into this project, I would like to take
this opportunity to express my thanks for your contribution to the development of such an invaluable tool for organic chemists.

PM




On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak <pm@chem.psu.edu> wrote:
On 6/25/2010 4:51 PM, Greeves, Nick wrote:
> I have used smol files for vibration
> e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well
> without any server side settings.
>
> All the best
> Nick
> Sent from my iPad
Thank you very much for the example. Your case indeed clarifies the
behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with
smol files, and if you do not reload, you cannot access the surfaces.

Try the following: start any of the vibrations. Now stop it (check the
vibration check box twice). Now check if MO's are still in the menu and
what kind mep loads (not the one form smol, but one generated by Jmol).

This is exactly what I was trying to explain (I am new to Jmol).

That issue was not related to the MIME type question (although both were
about smol). The same happens on the desktop Jmol.

Thank you for your assistance.

PM



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phone: 507-786-3107


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-- 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