The platon crystallographic package - səhifə 13
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Prior to the application of the
SOLV PLOTfunction, atoms may be deleted using the
DELETE ATOMoption on the ORTEP menu.
Example - Solvent Accessible Volume
invoke: 'platon squeeze.res' and click on 'SOLV PLOT'.
Example - Ohashi-volume
1 - Invoke PLATON:
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
18.104.22.168 – 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. 22.214.171.124). 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:
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 126.96.36.199-1– 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 188.8.131.52) and CALC VOID (
184.108.40.206 - 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.
Special preconfigured versions of FLIPPER are FLIP SHOW (
Section 220.127.116.11), FLIP
Section 18.104.22.168), FLIPPER 25 (
Section 22.214.171.124) and STRUCTURE (
Sub-Menu #0 – (
Section 1.4.31) – Options
126.96.36.199 - 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 9for details and
examples of the FLIPPER procedure.
188.8.131.52 - 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 9for details and examples of the FLIPPER
184.108.40.206 – 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.
220.127.116.11 – 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
SHELXL97for structure refinement.
PLATONas an alternative for the
SYSTEM-Ssequence for automated
structure determination that is available only in the
Mac OS Xversion of
PLATON(with structure solution options including
Note: This new tool is under development.
18.104.22.168 – ADDSYM
Tool for the detection of missed or pseudo higher symmetry in data supplied in CIF, RES or
SPF format. See
Chapter 4for full details and examples.
Fig. 22.214.171.124.-1.Example of a structure that was published in the orthorhombic space group
Pbca but shown by ADDSYM to belong to the cubic space group Pa-3. The symmetry
operations in white are the ones for Pbca. The additional threefold axes are presented
in red. This side menu shows options to change various tolerances and to produce
either a display of the averaged structure or a RES file suitable to continue refinement
in the higher symmetry group. The KeepMon-I-n Toggle allows the algorithm to reain
I centering and n glides when that leads to closer to 90 degrees beta angles.
Keyboard Instruction options:
CALC ADDSYM (element_name/EQUAL) (EXACT) (SHELX/PLOT) (NOSF) (KEEP
) (ang d1 d2 d3 perc)
- element_name- Search for higher symmetry for specified element only.
- EQUAL- Search with all atom type treated as equivalent.
- EXACT- All atoms should fit for given criteria.
- SHELX- A new
shelxl.resfile is generated for the proposed space group
- PLOT- A PLUTON-plot of the averaged structure in the proposed space group is
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