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 <[email protected]> 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 <[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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>
>
> --
> 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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