Fig. 1.3.1.4-2
. Listing of various ring properties including the Cremer & Pople puckering
parameters.
The Ring-plot option shares a sub-menu with the Newman and Plane plot series options:
Sub-Menu #0 – ( Section 1.4.13) – Options
1.3.1.5 – Plane-Plot – Least Squares Plane Plots
This option loops over a series of projections of the structure on planar parts in the
structure. PLUTON and ORTEP Plots can be made with the current orientation matrix with
options on the side sub menu. Clicking on NextPlane brings in the next plane .
The Plane-Plot option shares a sub-menu with the Ring and Newman plot series options:
Sub-Menu #0 – ( Section 1.4.13) – Options
1.3.1.6 - POLYHEDRA – Plot
The POLYHEDRA plot sub-program ( Fig. 1.3.1.6-1) is loosely based on the STRUPLO
program code by Fischer (1985). The program will search for and display tetrahedra and
octahedra recognized in the structure of an inorganic compound. A number of parameters
can be overruled with the following keyboard instructions. Those instructions should be
executed before invoking the polyhedra plot instruction.
SET RANGE -minx maxx -miny maxy -minz maxz
The default OMIT OUTSIDE range is -0.01:1.01, -0.01:0.01, -0.01:0.01. This can be changed with
the keyboard instruction:
SET OMIT minx maxx -miny maxy -minz maxz
Parameters used in the search for tetrahedra (defaults are 109.0, 20.0, 1.62 0.2)
SET TET p1 p2 p3 p4
Parameters used in the search for octahedra (defaults 90.0, 20.0, 1.97, 0.4)
Sub-menu #0 – ( Section 1.4.30) – Options
Fig. 1.3.1.6-1 – Polyhedra plot style.
1.3.1.7 – ContourDif – Contoured Difference Density Map Plot
Data files needed name.res and name.hkl - SHELXL styled structural parameter and
reflection files or name.cif and name.fcf parameter and reflection files. See Chapter 7 for
details.
Sub-Menu #0 – ( Section 1.4.22) - Main Options
Sub-Menu #1 – ( Section 1.4.23) - Options
1.3.1.8 – Contour-Fo - F(obs) MAP
Data files needed: name.res and name.hkl - SHELXL styled structural parameter and
reflection files or name.cif and name.fcf parameter and reflection files. See Chapter 7 for
details.
Sub-Menu #0 – ( Section 1.4.22) - Main Options
Sub-Menu #1 – ( Section 1.4.23) - Options
1.3.1.9 – AutoMol-Fit - Automatic Residue Fitting
Fig. 1.3.1.9-1 – Structure with two crystallographically independent molecules (hifdop.spf)
An automatic attempt is made to fit two crystallographically independent molecules (e.g .
the two molecules in Fig. 1.3.1.9-1) in the crystal structure on one another (see also section
1.4.9.9). Both molecules should be chemically equivalent (i.e. equal number of atoms, the
correct atom type assigned and no hydrogen atoms missing). The automatic fitting algorithm
involves unique numbers that are assigned to all atoms in the structure based on network
topology. Topology numbers are listed in the connectivity table under the heading tnr.
Automatic fitting is attempted, using the quaternion fit technique, (Mackay, 1984), on the
basis of atoms with a unique and equivalent topology number in each molecule to be fitted.
Atoms that are not topologically unique in a molecule are not included in the fit calculation
(but shown in the subsequent plot). The published Mackay procedure fails for (close to) 180
degree fit rotations about an axis. The 180 degree situation is of course quite common in the
crystallographic setting. PLATON/FIT implements a special 'work-around' for this problem.
The fit is done of the first residue or its inverted image on the second residue: the best fit is
retained and displayed (along with the number of atoms on which the fit was based). By
default (i.e. without the specification of residue numbers), residue #1 is fitted on residue #2.
Other fit attempts should be specified explicitly with a keyboard instruction (e.g. 'FIT 2 3').
Hydrogen atoms are not included in the automatic fit, but included in the subsequent
PLUTON style display. Details on the fitting results are written to the listing files.
In the case that the molecules to be fitted have no or not enough unique atom pairs, fitting is
attempted assuming consistent atom numbering in both molecules.
The ORTEP tool provides an option to click on a set of atom pairs on which the fitting
should be based (see Section 1.4.9.8)
The Quaternion fit algorithm is also used as part of the NONSYM function. Assignment of
equivalent (corresponding) atoms is done differently there. Symmetrical molecules may
often be fitted automatically via that path.
A fit on an explicit subset (at least 5 pairs) of atoms can be done as well:
Example: FIT C1 C19 C2 C20 C3 C21 C4 C22 C5 C23
The fitted coordinate sets are written to a file compound_fit.spf suitable for display.
Example: A structure (Fig. 1.3.1.9-1) taken from the CSD in P21, Z = 4. [Data: hifdop.spf].
The AutoMolFit result is shown in Fig. 1.3.1.9-2
Fig. 1.3.1.9-2 – Quaternion Best fit of Inverted Molecule #1 on Molecule #2.
Quaternion Fit of Molecules from Different Sources
Molecules from different origin may be fitted by concatenation of their corresponding PDB
files. (Use the PLATON/PDB tool ( Section 1.3.7.14) to produce such files). The number of
atoms in both molecules may differ.
Example: A fit of the structure of sucrose from neutron data on that of X-rays
[Data: sucrfit.pdb]. The fit is shown in Fig. 1.3.1.9-1
Fig. 1.3.1.9 – Fit of the X-ray and neutron structure of sucrose (fitted with pdb style files)
1.3.1.10 – HKL2Powder - Simulated Powder Pattern from HKL-Iobs
A Powder pattern is generated for the supplied reflection file containing F(obs)**2 data
along with the cell and symmetry info in .res, .cif or .spf format. ( Fig. 1.3.1.10-1)
Example: use a name.res & associated name.hkl for the structure of interest.
I(obs) data are calculated from F(obs) or F(obs)**2 data and include the reverse application
of the Lp-correction factors. The reflection data are averaged first according to the Laue
symmetry associated with the space group symmetry as supplied. The number of missing
data is reported (commonly low order reflections, often not in the data set for various
reasons - e.g. behind the beam stop etc). Subsequently, the data set is expanded to a half
sphere of reflections (recorded in a file with extension .hkp).
A powder file is generated in CPI format on a file with extension .cpi
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