I'm not having that problem at all with my Spartan files. I look at a vibration:

frame 3; vibration on

then go back to frame 1 and check the MO:

frame 1; MO HOMO

Works fine. Certainly Jmol is never "no longer able to access Frame 1".
Maybe you are just not going back to frame 1?



On Wed, Jun 30, 2010 at 9:27 AM, Pshemak Maslak <pm@chem.psu.edu> wrote:
On 6/30/2010 9:32 AM, Robert Hanson wrote:Coming back to my related questions:

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


vdw surface mapped with MEP is the most common:

  isosurface vdw map mep

very pretty! And the MEP itself can be visualized, but that's not a common visualization.

  isosurface mep


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


sure -- just make one JVXL file for each MO. This can be done with a pretty simple script if you needed to. The JVXL format does allow for multiple orbitals, but I haven't implemented that. Actaully, I think at one point Jmol could output every MO, but that takes so long and the file is so big, so I think that didn't make it into the release version of Jmol.

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


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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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