On Saturday 04 October 2003 20:59, Peter Murray-Rust wrote:
> At 19:30 04/10/2003 +0200, Miguel wrote:
> > > On Friday 03 October 2003 23:13, Miguel wrote:
> > >> > A second thing is, that we need to be able to display more than one
> > >>
> > >> unit cell, but say 2x2x2 unit cells... with all content... Again,
> > >> this is were the iterators come in... here the iterator repeats the
> > >> process in the previous paragraph for each unit cell it has to
> > >> plot...
> > >>
> > >> So, this is new functionality ... Correct?
> > >
> > > Well, it was in Jmol b6, but at least new to the CDK based Jmol..
> >
> >So, you are saying that this functionality exists in b6?
> >What are the steps I need to go throughto see it in b6?
> >
> > >> If so, then educate me a little more on this. Is it the case that you
> > >> want the same atom structure repeated, but with a base at a different
> > >> offset?
> > >
> > > Correct.
> >
> >OK.
> >Then it seems to me that there is a better way to handle this.
> >All one needs to do is repeat the same atoms, but translated to different
> >positions in 3-space.
>
> This is necessary but may not be sufficient.
It really is a two loop process...
foreach unit cell in AxBxC {
foreach within_unit_cell_symmetry_operation in Spacegroup {
draw symmetry_unrelated_atoms
}
}
> The unit cell contains n
> copies of the asymmetric unit - normally a single molecule. n depends on
> the space group (of which there are 230) and ranges from 1 (P1) to 192
> (Fm3m).
Never realized it could be that many!
> There should be n symmetry operators given for the system (of which
> one is the identity operator x,y,z). These symmetry operators must then all
> be applied to the contents of the asymmetric unit. In general this will
> generate new atoms, although if rotation axes or inversion centres are
> present some atoms will translate onto themselves.
>
> As an example, take spacegroup P1bar (no 2). This contains two symmetry
> operators, x,y,z, and -x, -y, -z. Suppose the molecule was given with
> **fractional coordinates**:
> C 0 0 0
> O 0.2, 0.3 -0.1
>
> you would have to apply the second symmetry operation to get two new atoms:
> C 0 0 0
> O -0.2, -0.3 0.1
> The first new atom overlaps (is identical to) the original carbon and so
> can be omitted. The second O is bonded to the C, thus giving an O-C-O
> molecule.
>
> You can then translate this by 1,0,0 0,0,2, -1,2,-2, etc to generate new
> cells.
Which is the translation over the unit cell axes a,b,c...
> note that all symmetry operations *must* be on fractional coordinates. If
> you are given cartesian coordinates only then you cannot generate
> fractional coordinates unless you are given the cell axes as vectors (not
> just a,b,c,alpha, beta, gamma).
Note that CDK has methods to convert fractional <-> cartesian for atomic
coordinates and notional <-> cartesian for the axes...
> If you do not generate symmetry equivalent molecules you will end up large
> voids in the structure.
>
> Note also that it is possible that the molecule consists of polymers in 1,
> 2, or 3 dimensions. This requires the generation of bonds between
> molecules.
The current rebonding code is quite efficient, so we could just do a rebond on
the super cell AxBxC...
> We are currently writing code for this process and hope to have some
> generic code.
Peter, what code are you refering to here? Applying the spacegroup symmetry
operations?
Egon
--
PhD Molecular Representation in Chemometrics
Laboratory of Analytical Chemistry
http://www-cac.sci.kun.nl/people/egonw.html
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