Note:
Prior to the application of the
SOLV PLOT function, atoms may be deleted using the
DELETE ATOM option on the ORTEP menu.
Example - Solvent Accessible Volume
Data files:
squeeze.res
and
squeeze.hkl
.
invoke: 'platon squeeze.res' and click on 'SOLV PLOT'.
Example - Ohashi-volume
Data:
ohashi.cif
.
1 - Invoke PLATON:
platon ohashi.cif
2 - Set van der Waals Radius Co to 0.7 Angstrom with:
SET VDWR Co 0.7
2 - Delete the atoms of the 'reactive group' with ORTEP/Delete atom/End
3 - Click on
SOLV PLOT etc.
1.3.3.8 – CAVITY-PLT -A Routine for the Visualisation of Empty Spaces
VOIDS in a structure are located and represented by spheres with radii equal to the contact
radius to the nearest van der Waals surface (see
Fig. 1.3.3.8). This routine is modeled on but
not identical with the program CAVITY by A. Mugnoli (14th European Crystallographic
Meeting, Abstract 530, Enschede, 1992). Keyboard instruction:
CAVITY (radius[1.2]),
where 'radius' is the minimum void radius searched. The default van der Waals Radii
supplied by PLATON can be overruled with user-supplied radii (e.g. ion-radii) with the
'SET RADII' instruction.
Example Data: cavity.res.
Fig 1.3.3.8-1 – The result of the cavity algorithm as displayed with PLUTON/POVRAY.
More elaborate alternative algorithms for the analysis of solvent accessible voids in a crystal
structure are available through CALC SOLV (
Section 1.3.3.1) and CALC VOID (
Section
1.3.3.2)
1.3.3.11 - FLIP MENU - Charge Flipping Menu
This tool provides a menu interface to the FLIPPER routine (
Chapter 9) for structure
determination. Various parameters can be set or changed. This can be achieved by either
clicking in the proper boxes in the sub-menu or with keyboard instructions (e.g.
NTRY 10)
Special preconfigured versions of FLIPPER are FLIP SHOW (
Section 1.3.3.12), FLIP
PATT (
Section 1.3.3.13), FLIPPER 25 (
Section 1.3.3.14) and STRUCTURE (
Section
1.3.3.15).
Sub-Menu #0 – (
Section 1.4.31) – Options
1.3.3.12 - FLIP SHOW - Visualization of the Charge Flipping Process
Charge Flipping in this version starts with all phases zero. An attempt is made to solve the
structure starting from a pseudo Patterson map (based on ABS(Fobs)) and a maximum of
5000 flip cycles. The progress of the routine is displayed graphically as the result of a peak
search display and in terms of the change of the R-value. See
Chapter 9 for details and
examples of the FLIPPER procedure.
1.3.3.13 - FLIP PATT - Single Starting Point Charge Flipping
Charge Flipping in this version starts from initial Phases set to Zero. An attempt is made to
solve the structure starting from a pseudo Patterson map (based on ABS(Fobs)) and a
maximum of 5000 flip cycles. See the
Chapter 9 for details and examples of the FLIPPER
procedure.
1.3.3.14 – Flipper 25 - Multiple Starting Point Charge Flipping
This is a multiple starting point version of FLIPPER with random phases assigned to
reflections. Up to 25 starting points are attempted with a maximum of 250 flips per attempt.
1.3.3.15 – STRUCTURE? - From Data to Refined Structure by Charge Flipping
This tool attempts a fully automatic ab-initio structure determination sequence based on an
implementation of the Charge Flipping Algorithm (Oszlanyi & Suto, 2004, 2005) for
structure solution and
SHELXL97 for structure refinement.
STRUCTURE? is
implemented in
PLATON as an alternative for the
SYSTEM-S sequence for automated
structure determination that is available only in the
LINUX and
Mac OS X version of
PLATON (with structure solution options including
SHELXS86,
SHELXS97,
SIR97,
SIR2004 and
DIRDIF99).
Note: This new tool is under development.
