are you using the applet or the application?
Sebastian Schwieger wrote:
>Hi Bob,
>
>I'm using Gaussian03 output.
>Is there a example or tutorial on how to to implement the use of
>functions in Jmol.js?
>
>Thanks,
>Sebastian Schwieger
>
>Bob Hanson schrieb:
>
>
>>Some preliminary work related to this was done. For Mopac and Spartan
>>files, vibration information is available via Jmol.js using the
>>jmolGetPropertyAsArray() function:
>>
>>VibrationData = jmolGetPropertyAsArray("auxiliaryInfo").vibration
>>
>>Then VibrationData[0] is the data for the first vibrational mode,
>>VibrationData[1] is the data for the second vibrational mode, etc.
>>Within each of those, [0] is for the first atom, [1] is for the second
>>atom, etc.
>>Within each of those, [0] is for x, [1] is for y, and [2] is for z
>>
>>So the vibration vector for the 3rd vibrational mode, atomno=2 is
>>
>>VibrationData[2][1][0],VibrationData[2][1][1],VibrationData[2][1][2]
>>
>>Then you can do with that whatever you want. Similarly,
>>
>>FrequencyData = jmolGetPropertyAsArray("auxiliaryInfo").VibFreqs
>>
>>This could be expanded to the other model types easily enough if desired.
>>
>>What file type are you using?
>>
>>Bob
>>
>>Sebastian Schwieger wrote:
>>
>>
>>
>>>Dear jmol users and developers,
>>>
>>>can I write xyz coordinates of a molecule corresponding to a
>>>displacement along a vibrational mode?
>>>I can animate the vibration, but did not figure out how to export the
>>>animated structure. Actually, I don't need the animation, but the two
>>>structures corresponding to the largest amplitude.
>>>
>>>Any help is appreciated.
>>>
>>>Sebastian Schwieger
>>>
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>>>
>>>
>>>
>>
>>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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