Re: [Jmol-users] ellipsoid that envelops a model

[Martin G. <mar...@go...>]

On Mon, Feb 11, 2013 at 5:39 PM, Robert Hanson <ha...@st...> wrote:

> 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
>

Sorry for not answering anymore to this subject. Actually, I gave it try by
using the bounding box axes for the ellipsoid, and it fitted quite well.
But I preferred using spheres because it looked more smooth and regular,
when having a lots of compounds.

Best regards,
Martin


>
>
>
>
>
>
>
> On Mon, Feb 11, 2013 at 10:03 AM, Oliver Stueker <
> rev...@us...> 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 <ha...@st...>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 <
>>> mar...@go...> 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:
>>>> gue...@in...
>>>>
>>>>
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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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>
>
> --
> 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
>
>
>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
> http://p.sf.net/sfu/sophos-d2d-feb
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> --
> Dipl-Inf. Martin Gütlein
> Phone:
> +49 (0)761 203 8442 (office)
> +49 (0)177 623 9499 (mobile)
> Email:
> <https://lists.sourceforge.net/lists/listinfo/jmol-users>
> gue...@in...