Dear Paul,
As you suggest, small molecule crystallographers are used to such
complicated situations and often use SHELXL for the purpose. Since you
fortunately have 1.0A data you could do the same, first using pdb2ins to
convert your PDB file to a SHELXL .ins file. You will need to use PART
instructions to define which atoms belong to which disorder component.
Then you will probably need DFIX or SADI distance restraints for the
overlapping atoms and RIGU for the anisotropic displacement parameters.
SHELXL and pdb2ins can be obtained as part of CCP4 or via the SHELX
homepage shelx.uni-goettingen.de
Best wishes, George
On 02/21/2017 07:13 PM, Paul Paukstelis wrote:
We've been working on a high resolution (1.0 A) DNA structure that has
several coordinated magnesium ions that have complete octahedral
geometry via water or phosphate oxygens but are clearly in multiple
conformations (which is related to the multiple conformations of the
coordinating phosphates). Is there a _proper_ way to handle this
scenario? Should the ions/waters be modeled as independent atoms with
fractional occupancy, or should they be identified as atoms with
alternate conformations? The latter case can get complicated for the
waters as the overlap can make it quite ambiguous in some cases as to
which two water pairs should be associated as the alternate
conformers. Perhaps it is a minor point, but I thought there might be
some kind of convention in the small molecule community where this is
sure to crop up more often.
Thanks in advance,
--paul
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
