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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