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On Tuesday 17 February 2004 15:29, Miguel Howard wrote:
> But with your help we can get it cleaned up.
Right.
> > - - Did I do it right, to create cartesian coordinates, or does Jmol
> > handle fractional coordinates internally too?
>
> Jmol now knows how to handle fractional coordinates for the unitcell.
Excellent!
> There are a set of new routines to handle crystal unit cells:
>
> getNotionalUnitcell()
> returns null or a float[6] which is the notional unitcell
> This is the terminology that you were using in CDK.
>
> getCrystalScaleMatrix()
> returns null or a float[9] which is the 3x3 scale matrix
> for converting cartesian to fractional coordinates.
>
> This is essentially the three SCALEn records out of .pdb
> If it is too specific to .PDB then we should change it and
> make it more general.
>
> getCrystalScaleTranslate()
> This is null or a float[3]
> It is the translation component that is used to translate
> the orthogonal coordinates to the fractional coordinates.
>
> This is the U component from the SCALEn records from .pdb
> Again, if this is too specific to PDB then we should
> generalize it.
>
> > - - How should I set the unit cell info in CDKJmolAdapter?
>
> Change the CDKJmolModelAdapter so that it implements
>
> float[] getNotionalUnitcell(...) {
> ...
> return new float[] {a, b, c, alpha, beta, gamma};
> }
Only this one, or also the others?
> Q: What is the difference between "Notional Unit Cell" and "fractional
> coordinates"?
There are two bits of data with crystals, each for which there are two related
coordinate system:
1. the unit cell info:
cartesian (a.x, a.y, a.z, b.x, etc... axes as vectors in eucledian space)
and notional (a,b,c, alpha, beta, gamma)
2. the atomic coordinates
cartesian, matching the cartesian coordinates of the unit cell
fractional (or crystal) coordinates, matching the notional unit cell
coordinates
To get back to your question: they can't be compared ;) But they are
used together.
Egon
PS. did this meesage reach the mailling list?
- --
[EMAIL PROTECTED]
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
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