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 <p...@chem.psu.edu
<mailto:p...@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 <p...@chem.psu.edu
<mailto:p...@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
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St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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