SOLV F3D
(1.3.3.6) Display of VOIDS with the F3D Program
SOLV PLOT
(1.3.3.7) Graphical Display of VOIDS in the Unit Cell
Cavity PLOT
(1.3.3.8) Cavity Plot
FLIP MENU
(1.3.3.11) Charge Flipping Menu
FLIP SHOW
(1.3.3.12) Visualization of the Charge Flipping Process
FLIP PATT
(1.3.3.13) Single Starting Point Charge Flipping
FLIPPER 25
(1.3.3.14) Multiple Starting Point Charge Flipping
STRUCTURE?
(1.3.3.15) From Data to Refined Structure with Charge Flipping
1.2.4 – Symmetry Related Tools
ADDSYM
(1.3.4.1) Search for Missed Higher of Pseudo Symmetry
ADDSYM-EQL
(1.3.4.2) ADDSYM with all Non-Hydrogen Atom Types Treated Equal
ADDSYM-EXT
(1.3.4.3) ADDSYM with all non-H Atoms Fitting Higher Symmetry
ADDSYM-PLT
(1.3.4.4) Display the Proposed Higher Symmetry Model
ADDSYM-SHX
(1.3.4.5) Create a RES file for the Proposed Higher Symmetry Model
NEWSYM
(1.3.4.6) Derive Space Group from F(calc) Data
NONSYM
(1.3.4.7) Report Non-Crystallographic Symmetry
LePage
(1.3.4.8) Report Higher Lattice Symmetry Proposed by LePage Tool
DelRed
(1.3.4.9) Report Higher Lattice Symmetry Proposed by DelRed Tool
MOLSYM
(1.3.4.10) Report Molecular Symmetry
SPGRfromEX
(1.3.4.11) Report Proposed Space Group based on F(obs) Extinctions
ASYM
(1.3.4.12) Tool for Averaging Reflection Data
ASYMaverFR
(1.3.4.13) Tool for Averaging (including Friedel Pairs) Reflection Data
LePageTwin
(1.3.4.14) Tool for the search of Twinning Operation based on LePage
TwinRotMat
(1.3.4.15) Tool for the Detection of (non)Merohedradral Twinning
1.2.5 – Absorption Correction Tools
MULscanABS
(1.3.5.1) Multi-Scan Absorption Correction
ABSPsiScan
(1.3.5.2) Psi-Scan Absorption Correction
ABSTompa
(1.3.5.3) Analytical Absorption Correction
ABSGauss
(1.3.5.4) Numerical Absorption Correction
ABSXtal
(1.3.5.5) Crystal Size Optimization base on Psi-Scans
ABSSphere
(1.3.5.6) Spherical Absorption Correction
SHXABS
(1.3.5.7) Empirical Correction for Absorption
Xtal Habit
(1.3.5.15) Display of the Crystal Habit
1.2.6 – Report and Analysis Tools
Validation
(1.3.6.1) Full Crystal Structure Validation
ASYM-VIEW
(1.3.6.2) Display of Reciprocal Lattice Sections
FCF-Valid
(1.3.6.3) FCF Validation
DIFFourier
(1.3.6.4) Difference Density Map + Peak List
ANALofVAR
(1.3.6.5) Analysis of Variance
BijvoetPair
(1.3.6.6) Analysis of Bijvoet Pairs: Absolute Structure
ASYM-EXPCT
(1.3.6.7) Calculation of the Expected Number of Reflections
ASYM-Valid
(1.3.6.8) FCF Validation
SupplMater
(1.3.6.9) Creation of Tables with Bonds,Angles and Torsion Angles
EXPECT-HKL
(1.3.6.10) Estimate of the Expected Number of Reflections
CSD-CELL
(1.3.6.11) CONQUEST Search based on Cell Dimensions
CSD-QUEST
(1.3.6.12) CONQUEST Search based on the Residues in the Structure
StructTidy
(1.3.6.13) Structure Tidy Analysis Tool
StrainAnal
(1.3.6.14) Stain Analysis Tool
locCIF-acc
(1.3.6.15) Creation of a CIF with local Information Added
1.2.7 - Miscellaneous Tools
SYSTEM-S
(1.3.7.1) - Guided/Automatic Structure Determination Tool
FCF2HKL
(1.3.7.2) - Create SHELX HKLF 4 Style from FCF
Expand2P1
(1.3.7.3) - Create Expanded to P1 Coordinate Set (RES Format)
FCF-Gener
(1.3.7.4) - Create an FCF styled Fo/Fc File from Coordinate Data
HKL-Gener
(1.3.7.5) - Create SHELXL HKLF4 styled Reflection File
HKL-Transf
(1.3.7.6) - Transformation of HKLF4 data + Direction Cosines
EXOR-RES
(1.3.7.7) - Work-up of Raw Structure Solution Peak List
ANIS-RES
(1.3.7.8) - Interactive Tool for Marking Anisotropic Atoms (SHELXL)
Rename-RES
(1.3.7.9) - Interactive Tool for Atom Renaming in RES file
Auto-Renum
(1.3.7.10) - Automatic Renumbering of Atoms in RES file
SPF-eld
(1.3.7.11) - Create SPF Standard File from Input File Data
SHELX-res
(1.3.7.12) - Create RES Standard File from Input File Data
CIF-acc
(1.3.7.13) - Create CIF Standard File from Input File Data
PDB-pdb
(1.3.7.14) - Create PDB Standard File from Input File Data
CIF2SHELX
(1.3.7.15) - Create INS & HKL Files from CIF & FCF
1.3.1 – The PLATON Package Opening Menu Option Details
This section gives more information about the tools that can be invoked from the main
PLATON menu (
Fig. 0.1-1). It is an expanded version of the information that is also
provided with the on line help function that is displayed by right-clicking on menu items.
Note that with 'PLATON', depending on the context, either the complete program package
or the geometry tool is intended. The version date that is displayed above the main menu is
relevant as reference to the version of the program used.
Note: Not all clickable commands can be used one-after-the-other. Sometimes, and often to
be preferred, a RESET instruction will be needed.
The PLATON main menu comes with three selectable sub-menus on the side as is indicated
by the three sub-sections in the OptionMenu box (top-right). The default menu is #0. Other
sub-menu's are selectable by clicking in one of the other
box's. For more
details see the manual sections listed below.
Sub-Menu #0 – (
Section 1.4.10) – Main Options
Sub-Menu #1 – (
Section 1.4.11) – Parameter Tuning Options
Sub-Menu #2 – (
Section 1.4.12) – I/O Options
1.3.1.1 -
PLUTONauto – Path to PLUTON with PLATON Consistency
The PLATON subprogram tool PLUTON (See
Chapter 3; Fig. 1.3.1.1-1), a further
development of the original PLUTO program (Motherwell & Clegg), is a molecular
graphics tool that is designed for the study and display of molecules in their crystalline
environment. Vector graphics figures rather than raster graphics images are produced, both
on a display surface (X-Windows or equivalent) and as hardcopy (PostScript, HPGL).
A structural model does not need to represent a connected set as far as the refinement of the
structure is concerned. However, for the description of the structure and its graphical
presentation it makes sense that the atoms form a connected set with their centre of gravity
within the bounds of the unit cell. The default algorithms that are implemented in PLATON
and PLUTON for the collection of connected sets of atoms into molecules differ for
historical reasons to some extent. This may cause some unnecessary confusion. PLATON
therefore provides with the
PLUTONauto option a path to PLUTON that insures
consistency of ARU-codes (See
Section 2.4.3) in PLUTON with those given in the
PLATON/CALC listing and ORTEP presentation. This consistency goal is achieved with the
generation by PLATON of a new input file (SPF style) with the extension
.eld as an
intermediate that is subsequently used as input for the build-in PLUTON tool. This
structural parameter file (SPF) is saved for optional future use. The text NOMOVE
FORCED on the PLOT reflects the consistency with the PLATON tool.
In parallel, a file with extension
.def is generated. This file contains a set of PLUTON
instructions for a default 'straw style ball-and-stick' display of the input structure. The
.def
file is read by the program after reading the
.eld file and before user input.
Fig. 1.3.1.1-1
. Default PLUTON straw-mode drawing of the sucrose molecule in
the minimum
overlap orientation. Labels have been positioned automatically avoiding overlap
with atoms, bonds
and other labels. The three numbers in the corners, associated with either the X, Y or
Z symbol, are