The specification of the space group is optional.
The example run would produce a new file
compound.hkp
and a short terminal output when run as
platon compound.ins :
:: TITL N1848A
:: CELL 22.1829 9.1517 10.6597 90.000 105.758 90.000 2082.7
:: SPGR P21/n
Direct Cell axes and HKL Transformation Matrix
1.0000 0.0000 1.0000
0.0000 1.0000 0.0000
-1.0000 0.0000 0.0000
Coordinate Transformation Matrix
0.0000 0.0000 1.0000
0.0000 1.0000 0.0000
-1.0000 0.0000 1.0000
Transformation Matrix for SHELX Direction Cosines
0.0000 0.0000 1.0000
0.0000 1.0000 0.0000
-0.9848 0.0000 0.4805
:: HKLTRANS hkl on :compound.hkp
1.3.7.7 – EXOR-RES – Work-up of a Raw Structure Solution Peak List
A raw structure (e.g. coming from the structure solution program SHELXS as a
RES file)
containing both real and false peaks is cleaned up by removing false peaks and adding
missing peaks in a cycle of population refinements and analyses of difference density
Fourier maps. The EXOR tool was designed as part of the SYSTEM-S tool (see
Chapter 10
) but may also be called/used directly. The input data to be supplied are a
.ins (i.e. a renamed
.res) file along with an associate
.hkl file containing the reflection data. The alternative
terminal window command is
platon -E name.ins.
1.3.7.8 -ANIS-RES – Interactive Change from Isotropic into Anisotropic
This is an interactive tool for making isotropic atoms in a RES file anisotropic. An updated
RES file (with the extension
.new) for refinement with SHELXL is generated. The desired
change from isotropic to anisotropic is indicated by clicking on the associated atom in a
PLUTON drawing. Labels for anisotropic atoms are shown in RED. This function was
designed as part of the SYSTEM S tool for automated or guided structure solution and
refinement.
1.3.7.9 – Rename-res – Interactive Renaming of Atom labels in a RES File
Atom labels in a
shelxl.res style structured files can be changed interactively in a RENAME
loop using PLUTON tool for the interactive display and clicking on atoms to be renamed.
Renaming can be looped for global renaming or by clicking on individual atoms. A
keyboard RETURN/ENTER keeps the label as is. When a number is given in place of a
substitute label name, this number is concatenated with the current atom type. Renamed
atoms appear in green is the display. Temporary labels are generated when label conflicts
would occur (i.e. Renaming C10 into C1 when C1 already exists will automatically rename
C1 into a free label e.g. C999). The modified
RES file in written out with the
.new
extension. Alternatively, renaming can be invoked via the '
-r' switch e.g.
platon -r
sucrose.res. See also the Auto-Renum function (
Section 1.3.7.10).
1.3.7.10 – Auto-Renum – Automatic Renumbering of the Atoms in a RES File
Clicking on this button provides automatic atom label renumbering of a SHELXL RES file
(to be supplied with the
.ins extension) based on the molecular network topology. The result
is written in SHELXL
.res format. Note: Only labels on atomic parameter records are
changed.
1.3.7.11 – SPF-eld -
Create an SPF Standard File from Input File Data
Clicking on
SPF-eld will generate an
SPF styled file. (This is the free format structural
parameter file, native to PLUTON and PLATON). Alternatively, an SPF-style file can be
generated in the filter-mode. Example: generate a
.eld file from a
.cif:
platon -j sucrose.cif.
A
.eld file is usually renamed to a file with extension
.spf.
1.3.7.12 – SHELXL-res – Create a RES Standard File from Input File Data
Clicking on
SHELX-res will generate a
shelxl.res formatted file, e.g. from a
.cif or
.spf file.
The equivalent keyboard instruction is
CALC SHELX NOSF. Additional instructions will
make this file suitable for a refinement run with SHELXL97, given the availability of a
.hkl
file (optionally to be generated from a
.fcf file with the
FCF2HKL tool (
Section 1.3.7.2))
Alternatively, a shelxl-style
.res file can be generated in the filter-mode: Example: generate
a
.res from a
.cif: platon -g sucrose.cif
The
NOSF keyword suppresses the explicit generation of SFAC lines that include scattering
data.
A RES file supplied as
name.ins will produce a
name.res with atoms forming a connected
set.
1.3.7.13 – CIF-acc -
Create a CIF Styled File from Input File Data
Generation of a CIF File (Acta Cryst. C/E style) from the supplied input data file to be
completed by manual editing with additional data. This tool can be useful when a CIF
structured file is needed where only an SPF or RES structured file is available. In the last
case there are no standard uncertainties available. With a CIF as input, a new CIF is created
with some additional data added such as the moiety formula. Symmetry operations are
standardized. Bond distances, bond angles and torsion angles are recalculated based on the
variances associated with the positional parameters. Also a hydrogen bond table is
appended.
1.3.7.14 – PDB-pdb –
Create a PDB Styled File from Input File Data
Clicking on
PDB-pdb on the PLATON main menu will generate a
PDB styled file, based
on the current parameter input file (e.g. a CIF file or a RES file). Some software requires
PDB structured data as input. Records in this file have a fixed format. The coordinates are