1.3.2.12 - AngLsplLin - Interactive Calculation of the Angle between a Least
Squares Plane and a Bond.
A click on this menu-option brings up an ORTEP drawing with clickable atoms and
applicable option sub menu. The molecule can be rotated to a suitable orientation. The red
sub menu item
LsplWithEnd on the right indicates that the program is ready to receive the
atom names that will determine the least-squares plane by clicking on the corresponding
atom names. This sequence is ended and the sequence for the two bond atoms started by
clicking in the
With side-menu box. The second sequence is ended (and the calculation
initiated) by clicking in the
End field. Alternatively, an instruction similar to
LSPL c3 c4 c5
WITH c1 c2 could be issued from the keyboard. Atoms are treated with unit-weight by
default in the plane calculation. Alternatives are weighting based on atomic weights or
standard uncertainties (su) of the atomic coordinates. The default weighting scheme may be
changed using the
(UAE)WLSPL button on the side menu.
1.3.2.13 – CremerPople - Interactive Calculation and Display of Cremer & Pople
Ring-Puckering Parameters.
A click on this menu-option results in a display loop over the rings found in the structure. A
subsequent click on the
CremerPople button in the GEOM sub-menu will give a summary
display of the ring geometry and puckering analysis results.
Note: Full details of the analysis can be found in the associated
.lis and
.lps files.
1.3.2.14 – Bond Valence Analysis
A click on this menu-option invokes a
CALC COORDN loop preceding to the actual bond-
valence analysis (Brown, 2002). Full details of the analysis can be found in the
.lis and
.lps
files. The reported atom valence is tentative and should be used with care.
1.3.2.15 – HFIX-RES - Generate SHELXL-Style HFIX Instructions
This is a tool that is primarily used as part of SYSTEM-S (
Chapter 10) but is also
accessible as a 'stand-alone' tool. HFIX instructions suitable for SHELXL refinement are
generated and included in a modified
RES file. The modified
RES file in written out with
the
.new extension and should be renamed to
.ins to be used. The HFIX feature can be
invoked with a
.res file from the PLATON main-menu by clicking on the 'HFIX RES'
button. HFIX-RES is also available from one of the PLUTON sub menu's. However, that
will work only when PLUTON has been called DIRECTLY through PLUTONative or as
'
platon -p' and not indirectly through PLUTONauto (since in that mode PLUTON is run on
an internally generated non-res file). The actual H-atom coordinates are not calculated by
PLATON but can be generated subsequently using the (renamed to .ins) '.new' file as input
to SHELXL.
Various 'HFIX' entry modes are available. (The assigned numerical values are those defined
by SHELXL).
1. As Keyboard instruction in PLUTON: e.g. HFIX C8 137
2. As the generic keyboard or 'menu' instruction 'HFIX' (in PLUTON or SYSTEM S).
In that mode, atoms to HFIX can be clicked on or a loop can be started over all
relevant atoms. The atom that is currently under consideration is displayed with a
RED label along with the suggested HFIX code (see SHELXL manual) in square
brackets. [0] indicates NO HFIX.
Suggested values can be adopted by hitting
RETURN or overruled by entering the
desired value. A negative value should be entered to avoid addition of H-atoms.
'Auto' will introduce H-atoms with the suggested HFIX types without further
questions asked.
1.3.3.1 – CALC SOLV – Determine the Solvent Accessible Volume
Fig. 1.3.3.1-1. Example SOLV and VOID output. The unit cell contains four (symmetry
related) voids. Details are listed for all. Two grid points are reported under #gridpoint and
two volumes under Vol: The number in [] corresponds to the number of grid points (and
volume) that have the property of being at least the probe-radius (Default 1.2 Angstrom)
away from the van der Waals surface of the nearest atom (the Ohashi volume). The second
number corresponds to the number of grid points (and volume) in the solvent accessible
region. For each void the centre of gravity is reported along with the eigenvectors and
eigenvalues of the second moment of the grid point distribution.
PLATON offers two options for the detection and quantitative analyses of solvent accessible
voids in a crystal structure:
- VOID, a compute intense version, useful mainly when, in addition to the detection of
solvent areas, a packing coefficient (Kitaigorodskii, 1961) is to be calculated and unit cell
sections to be listed. The sections show the regions within the van der Waals surface, the
solvent accessible void region and the cusps in between.
- SOLV, a faster shortcut version of VOID (at the price that no packing coefficient is