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access to the full co-variance matrix such as SHELXL. However differences are never
dramatic. Statistical Information on the variation of bond distance values for similar bonds
have been collected in a separate table.
Least Squares Planes. PLATON automatically searches for planar parts and rings in a
structure. Least squares planes are calculated for them and listed along with the distances a
nearly atoms to those planes. Two plane equations are given: one in terms of Angstrom
coordinates and one in terms of fractional coordinates. The latter are often more useful when
the distance of a symmetry related atom to a given plane is of interest. Such a distance is
easily calculated as the value obtained by substituting the fractional x,y,z value in the
expression P * x + Q * y + R * z – S. The above listing of planes is followed by a listing of
angles between the planes and the angle of the bond list with the planes.
Rings. At this point the up to 24 membered rings that are found in the structure are listed
along with a detailed analysis of the puckering. The current structure has none. This part of
the analysis will be detailed with another example.
Non-bonding Contacts. Short intra and intermolecular contacts are listed per molecular
residue along with the associated symmetry relation. Short contacts are identified on the
basis of tabulated or supplied van der Waals radii. The short contacts are analyzed in the
next tabulation in terms of the number of short contacts of a given asymmetric residue unit
(ARU) to neighboring ARU's. The short contacts are further analyzed in terms of clusters
and networks of molecules.
Hydrogen Bonds. This is a special type of short contacts. The geometries of all hydrogen
bonds conforming default use user defined criteria are tabulated and analyzed in terms of
linear, bifurcated or trifurcated. Hydrogen bonds connect molecules into frameworks of
dimensionality one (chains), two (planar nets) or three (3D-networks). A similar analysis is
done for cooperative chains of the type ~O-H...O-H...O-H...O~ and circuits
Coordination Sphere. The coordination sphere up to 3.6 Angstrom for all non-carbon or
hydrogen atom is analyzed. Phi and mu in this listing are the polar coordinates of the
outgoing bonds. In case of a 5-coordinated atom, the position on the the Berry pseudo-
rotation pathway between square pyramidal and trigonal bi-pyramidal is reported. In case of
a metal, the valence of the central atom is predicted based on Bond Valence theory.
Solvent Accessible Voids. A search is done for solvent accessible voids in the supplied
structure model. No such voids are found in the current example. For more details see .
Final Difference Density Map. A difference map is calculated and analyzed for unresolved
density when reflection data are supplied. Density maxima and minima are listed along with
the nearest neighbor atoms within 3.2 Angstrom. High absolute density maxima may be
indicative for wrong atom type assignment, missing atoms, disorder, twinning or absorption
Validation Report. A summary of the structure validation report is appended (with a copy
on ambi.chk). The file
ambi.ckfcontains the FCF validation report.
Structure Analysis Summary. Numerical data on the structure analysis are collected in a
APPENDIX VII – HELENA
This is a tool within PLATON with no entry in the main menu. It is reachable only via the
-koption on the PLATON command line and requires the specification of a raw CAD4 data
platon -k helena.cad).
APPENDIX VIII – COMPARE: Compare two FCF Files
This is a tool within PLATON with no entry in the main menu (
Fig. VIII-1). It is reachable
only via the
-doption on the PLATON command line and requires the specification of two
FCF files to be compared. (e.g.
platon -d file1.fcf file2.fcf). It was designed to detect cases
of fraud but can also be helpful for scientific analysis purposes. The comparison can be
either on a linear or a log-log scale.
Fig. VIII-1. Scatter Plot for the comparison of two data sets.When data sets are identical, all yellow
dots should be located on the red diagonal.
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