Re: [Jmol-developers] definition of center of a molecule

[Fabian D. <fab...@wa...>]

On Fri, 2002-11-15 at 23:20, mth wrote:
> In jmol the center of the molecule is the point about which the molecule
> is rotated.
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> Currently the center is the geometric center of the molecule based upon
> the cartesian coordinates stored in the file. That is, the center x
> coordinate is the average of the minimum x coordinate and maximum x
> coordinate in the file. y and z are the same. Note that this is somewhat
> arbitrary ... if the molecule coordinates are rotated file, then you will
> get a different center.
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> It is probably not an important point, but as I am working on the code I
> am wondering whether or not this is the best definition.
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> Three other ideas come to mind:
>  1. the center of gravity of the molecule (using atomic weights)
>  2. the unweighted "center of gravity" (all atoms weigh the same)
>  3. the center point of the smallest sphere which would enclose the molec=
ule

I am also thinking of other schemes:=20

*ask the user to pick an atom which will be the center of rotation.
*ask the user to enter a coordinate.=20
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> As I write this, I realize that these points would also change depending
> upon the orientation of the atoms in the file.
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> So maybe it doesn't matter. What do you think?

Maybe we should add a new dialog with this features:

-select a rotation scheme
-fine rotations: do a rotation of x degree about a given axis (x, y, z
or user input).

=46rom the abinit workshop I know that users are very interested in that
kind of feature.

Fabian

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> Miguel
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Fabian Dortu

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e-mail : Fab...@wa...
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