Re: BMRB diffusion tensor saveframes. -- November 25, 2009 - 18:43

Hi,

The tag _Tensor_list.Geometric_shape as in your second example would 
work well as long as the values in the enumerated list are mutually 
exclusive. It would not be good to have one entry with a value of 
'sphere' and another with the value of 'isotropic'.

Would this work:

_Tensor_list.Geometric_shape (sphere, spheroid, oblate spheroid,
         prolate spheroid, rhombic)
_Tensor_list.Shape_homogeneity (isotropic, anisotropic)

Then 'anisotropic' groups everything except 'sphere' so that they can 
all be selected in a single query. Of course 'sphere' and 'isotropic' 
are a bit redundant. I suggest 'rhombic' instead of 'ellipsoid' as this 
seems to be the more defining term used by many people.

It would seem that having both items like 'spheroid' and 'axial 
symmetry' as enumerations to the same tag since they are equivalent by 
the definition below would be confusing.

Regarding the inclusion of coordinates, I would tend to favor including 
all of the coordinates for the model used. Although not required, it 
provides context for users when they download the file for their own 
calculations.

Cheers,
Eldon

Edward d'Auvergne wrote:
> Hi,
>
> Having 2 tags to serve this purpose is a good idea.  I would suggest
> then, to match the physics rather than anything else:
>
> _Tensor_list.Geometric_shape (sphere, spheroid, oblate spheroid,
> prolate spheroid, ellipsoid).
> _Tensor_list.Isotropy (isotropic, anisotropic, axial symmetry, oblate
> axial symmetry, prolate axial symmetry, rhombic).
>
> What do you think?  Here:
>
> sphere = isotropic,
> spheroid = axial symmetry,
> oblate spheroid = oblate axial symmetry,
> prolate spheroid = prolate axial symmetry,
> ellipsoid = rhombic.
>
> Or maybe this would be best:
>
> _Tensor_list.Geometric_shape (sphere, spheroid, oblate spheroid,
> prolate spheroid, ellipsoid, isotropic, axial symmetry, oblate axial
> symmetry, prolate axial symmetry, rhombic)
> _Tensor_list.Tensor_shape_homogeneity (isotropic, anisotropic)
>
> If these are closed enumerations, then automatic parsing by downstream
> programs will be possible.
>
> Cheers,
>
> Edward
>
>
> 2009/11/23 Eldon Ulrich <elu@xxxxxxxxxxxxx>:
> > Hi,
> >
> > The usefulness of having isotropic and anisotropic as main headings is that
> > it allows one to query for all anisotropic tensors without the need to know
> > the full list of possible anisotropic shapes. This could be solved using two
> > tags in at least two ways:
> >
> > 1) _Tensor_list.Tensor_shape (isotropic or anisotropic)
> >   _Tensor_list.Tensor_sub_shape (rhombic, sphere, oblate spheroid, etc.)
> >
> > 2. _Tensor_list.Tensor_shape (rhombic, sphere, oblate spheroid, etc.)
> >   _Tensor_list.Tensor_shape_homogeneity (isotropic, anisotropic)
> >
> > Other suggestions?
> >
> > Eldon
> >
> > Edward d'Auvergne wrote:
> > > 2009/11/19 Eldon Ulrich <elu@xxxxxxxxxxxxx>:
> > > > Hi,
> > > >
> > > > The suggestions for the tensor saveframe overall look fine. Instead of
> > > > including the shape of the tensor in the '.Details' tag or the
> > > > '.Speroid_type' tag, I would suggest creating a tag
> > > > '_Tensor_list.Tensor_shape' tag with enumerations like 'isotropic,'
> > > > 'anisotropic,' 'rhombic,' 'anisotropic prolate,' and others.
> > > I would suggest a different list as the term anisotropic includes the
> > > rhombic tensors.  This is what I've done in relax to remove ambiguity
> > > - I've used the pure names from geometry:
> > >
> > > sphere: http://en.wikipedia.org/wiki/Sphere
> > > spheroid:  http://en.wikipedia.org/wiki/Spheroid
> > > oblate spheroid: http://en.wikipedia.org/wiki/Oblate_spheroid
> > > prolate spheroid:  http://en.wikipedia.org/wiki/Prolate_spheroid
> > > ellipsoid:  http://en.wikipedia.org/wiki/Ellipsoid
> > >
> > > This is totally unambiguous and independent of the numerous
> > > (inconsistent) definitions used for tensors throughout NMR.  Of course
> > > the ellipsoid shape includes the spheroid and sphere, and the spheroid
> > > includes the sphere.  But generally sphere = 3 equal eigenvalues,
> > > spheroid = 2 equal eigenvalues, and ellipsoid = all 3 eigenvalues
> > > different, therefore an ellipsoid with 3 equal eigenvalues is called a
> > > sphere.  Note that the terms 'isotropic' and 'rhombic' are unambiguous
> > > though.  I would strongly recommend against allowing 'anisotropic'
> > > because some people think of this as a spheroid, while others think of
> > > it as anything non-isotropic - the correct definition.
> > >
> > >
> > > > A full list of
> > > > tags for the saveframe is given below. I hope I have them all in there. I
> > > > think having one general saveframe for tensors is fine and then in one
> > > > file
> > > > using separate tensor saveframes where appropriate would work. The list
> > > > of
> > > > tags in the loop has become quite long, but only those relevant to the
> > > > specific type of tensor need to be used.
> > > This makes it quite powerful then!  I'll keep you informed if new tags
> > > are needed to store all relevant information.
> > >
> > >
> > > > The tensor saveframe would go in supercategory 8 for structure and the
> > > > Shielding_tensor saveframe will be obsoleted.
> > > Ok, I will code bmrblib accordingly.
> > >
> > > Cheers,
> > >
> > > Edward