On 6/30/2010 10:38 AM, Jeff Hansen wrote:
OK.  So ignore my previous post.  I was thinking you wanted to view the vibrations and MOs simultaneously.  Obviously not what you want.  You said that "MO #" gives a message that no MO coefficient data is available.  This would be true unless you are in model 1.  I think just stopping vibrations will leave you in whichever model was showing when you stopped vibrations.  Unless that happened to be the first model then you wouldn't have any MOs available.  Switch to model 1 and the MOs should be available.

What other surfaces are you interested in?
Thanks. I think your comments helped me to figure out how that works. There is no bug: it is how it is designed: one has to (manually i.e. through menu or script) return back to the frame with MO info.
As you have said stopping vibration does not automatically return Jmol to frame (model) 1 (where MO's are).

I am mostly interested in setting Jmol in such a way that is easily accesiblke to students. I do not want the Jmol "mechanics" to divert from the chemistry contents.

Since Spartan easily calculates various surfaces (density(bonds), density(HOMO) or density(LUMO to name the few, I was wandering if they are written into smol files and whether they are accessible through Jmol.

Thanks!

PM.






***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
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On Jun 30, 2010, at 10:27 AM, Pshemak Maslak wrote:

On 6/30/2010 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).
Thanks. I am new to Jmol, but not that new. :-)   I have no problems individually visualizing any of the vibrations, or MOs, or mep surfaces from smol files..

The problem (possibly a bug as you have suggested) is that once vibrations are visualized the MOs or mep are no longer accessible without reloading the smol file.  I am guessing that the "frame" that holds MO and mep data  is not longer read by Jmol after one of the vibrational frames was read. For example, after stopping vibrations (vibration off) "MO #" would give a message that no MO coefficient data is available for this frame, and no MO is displayed. When I choose all vibrational frames (from the menu) I get the same error message, but the MO loads! 


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
Coming back to my related questions:

Can any other surfaces (in addition to MOs and mep) be visualized through smol files?

Can Jmol write jvxl files with multiple surfaces (for example selected MOs)?

Thanks for all your help.

PM


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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Northfield, MN 55057
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it is better to take what answer we get.

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