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.
>
>
Hmm. When I implement that, it doesn't work as expected. And if you think
about it, I don't see how it would. The weighted sum of positions gives
more of a 'density' than an 'extent'. I might try it with points from the
vdw surface.
> 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:
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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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>
>
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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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