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Ethan Merritt wrote:
However, when individual atoms are modelled anisotropically, there
is an apparent bond-length compression that arises from failing to
apply a correction to the distance between the centroids of two
ellipsoids. Programs such as shelx apply this correction when
reporting bond lengths.
Ethan,
To put the record straight, shelxl does not correct bond lengths for
libration, but a program I wrote many years ago (called xp) that is
still sometimes used by small-molecule crystallographers does.
In fact the correction is negligible for large molecules, but is
important for small molecules and ions such as sulfate and phosphate
that one often needs to handle in protein structures. For this reason I
do not recommend restraining the bond lengths in these ions to
particular target values (DFIX in shelxl) but prefer to apply the
restraints that e.g. all S-O distances are equal and all O..(S)..O
distances are equal (SADI in shelxl). This also takes into account the
effect of pH on the P-O distances in phosphates! Alternatively in shelxl
one can apply the 'variable metric' rigid group constraint (AFIX 9) that
keeps the angles and the relative bond lengths fixed but allows the
group to shrink (or expand) as a whole.
George
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
