Just to clarify. It sounds like the problem Pshemak is having is that when he
looks at the vibrations, it is actually switching to another frame or model.
These other frames or models do not contain the MOs. The MOs are still there
(associated with the first model - or is model 1 the second model?). To see
the MOs along with the other models I suppose they could be copied over using
some javascript? However, it seems this would look funny with some static MO
with the atoms moving relative to it. If what Pshemak wants is to animate
through the vibration models and have an MO associated with each vibration
model which has been calculated for that model that will be a tough thing to
do. It is no longer a Jmol issue but rather how to get Spartan to calculate an
MO for each vibration model it is generating then output that in a way that
Jmol could read and animate. Probably possible, but I'm not sure exactly how
to do it.
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[email protected]
***********************************************
On Jun 30, 2010, at 9:32 AM, Robert Hanson wrote:
> 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 <[email protected]> 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 <[email protected]> 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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>>
>> --
>> 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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>
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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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