> My confusion lies with whether the translation 555, 565, etc. is to be
> applied after the exact application of the symmetry operation (which very
> often moves an atom into another unit cell) or after normalization back into
> the 555 unit cell, and if so, how exactly that normalization is to be
> performed for atoms very near cell boundaries. I'm not convinced Jmol can
> reproduce that if normalization is involved.
It is a long time ago that I did something similar, so I am not an expert
anymore in this. But I think you will have to normalise (put all atoms back
into one cell) first and then treat the special positions (remove all exactly
overlapping atom positions). Then, I think everything should be okay. Atoms
near the cell boundaries (or indeed on the boundary itself) will be move one
unit cell away when you add 1 to their position.
Christian
On 25. Sep, 2014, at 03:09, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
> On Wed, Sep 24, 2014 at 3:49 AM, Brian McMahon <b...@iucr.org> wrote:
> Hi Bob, Christian
>
> loop_
> _geom_bond_atom_site_label_1
> _geom_bond_atom_site_label_2
> _geom_bond_distance
> _geom_bond_site_symmetry_1
> _geom_bond_site_symmetry_2
> _topos_geom_bond_publ_flag
> X1 X2 1.342(4) 1_555 1_555 yes
> X1 X2 1.439(3) 1_555 2_565 yes
> X2 X3 1.512(4) 1_555 1_555 no
>
>
> It has never been clear to me what site_symmetry means in these descriptions,
> and Jmol certainly ignores them. Instead, it will bond any X1 X2 atoms (in
> this case) with 1.342+-0.004 or 1.439+-0.003 distance ranges regardless of
> the site_symmetry.
>
> My confusion lies with whether the translation 555, 565, etc. is to be
> applied after the exact application of the symmetry operation (which very
> often moves an atom into another unit cell) or after normalization back into
> the 555 unit cell, and if so, how exactly that normalization is to be
> performed for atoms very near cell boundaries. I'm not convinced Jmol can
> reproduce that if normalization is involved.
>
> Is that an issue in this case?
>
> Bob
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