That sounds about right. Why do you care about the atomic masses? I think
in this application, you would just ignore those, right?
So Martin, you ALMOST could do this in Jmol. Right now we do almost that
calculation with the COMPARE command, and a minor tweak would allow us to
use it for this purpose.
I think you are suggesting:
ellipsoid {atom set}
Should we give that a try? Oliver, would it be useful to allow an option
that includes atomic masses?
Bob
On Mon, Feb 11, 2013 at 10:03 AM, Oliver Stueker <
[email protected]> wrote:
> Hi,
>
> How important is it that the molecule is completely within the ellipsoid?
>
> I have seen the use of the "inertia equivalent ellipsoid" to characterize
> molecules.
> e.g. MDanalysis [1] calculates the principal axes from the moment of
> inertia [2].
> The resulting eigenvectors can be used to construct the inertia equivalent
> ellipsoid.
>
> That might be a useful addition to Jmol as well.
>
> Oliver
>
> [1] http://code.google.com/p/mdanalysis/
> [2] source-code of
> AtomGroup.principalAxes()<http://code.google.com/searchframe#5tmZDZKD7HI/package/MDAnalysis/core/AtomGroup.py&q=principalAxis%20package:mdanalysis%5C.googlecode%5C.com&l=967>
>
> On Mon, Feb 11, 2013 at 12:10 PM, Robert Hanson <[email protected]>wrote:
>
>> The closest I could suggest would be using the dimensions of a boundBox.
>> You are right that there is significant math if you want "the tightest
>> ellipsoid" -- I'm guessing that's an Eigenfunction problem.
>>
>>
>> On Mon, Feb 11, 2013 at 4:22 AM, Martin Guetlein <
>> [email protected]> wrote:
>>
>>> Hi,
>>>
>>> is there a convenient way to draw an ellipsoid that envelops a model?
>>>
>>> This command would draw a sphere that envelops a model:
>>> > ellipsoid ID <myEllipsoid> AXES {<modelRadius> 0 0} {0 <modelRadius>
>>> 0} {0 0 <modelRadius>} CENTER <modelCenter>
>>> But most compounds are sort of longish, and it would be nice to use an
>>> ellipsoid for that (I fear that there is a lot of ugly math involved to get
>>> that done, though).
>>>
>>> Cheers,
>>> Martin
>>>
>>> --
>>> Dipl-Inf. Martin Gütlein
>>> Phone:
>>> +49 (0)761 203 8442 (office)
>>> +49 (0)177 623 9499 (mobile)
>>> Email:
>>> [email protected]
>>>
>>>
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>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> 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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>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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