1. PLATON TUTORIAL A.L.Spek, National Single Crystal Service Facility,
Utrecht, The Netherlands.

2. What is PLATON A Multipurpose Crystallographic Tool
Compatible with and Complementary to P.D. SHELX & Bruker-AXS SHELXTL
‘Public domain’ (I.e. free-of-charge for academics, License Fee for Profit Org.)
Available on UNIX/LINUX, MS-Windows & MAC-OSX Platforms

3. Multipurpose Crystallographic Tool
Automatic Geometry Analysis & Listing.
Molecular Graphics (PLUTON, ORTEP,Fourier)
Absorption Correction Tools(MULABS,TOMPA)
ADDSYM - Check for Missed Symmetry.
SQUEEZE – Disordered Solvent Handling.
Generation of Powder Patterns.
Structure Validation (part of IUCr CHECKCIF).
System-S, Automated Structure Determination.

4. EXAMPLE Input Shelx Style: sucrose.res
(Alternatively: .cif,.pdb,.dat,.spf style)
Invoke PLATON (UNIX: Platon sucrose.res)
Opening Menu (4 areas)
Automatic ORTEP style PLOT
Automatic PLUTON style PLOT
Simulated Powder Pattern
H-Bond Table

10. PLATON/ADDSYM ANALYSIS
Example run on 9163 Z’ = 2 Organic structures present in the in CSD.
ADDSYM  466 Hits (Missed or Pseudo Symmetry Cases)
Some Missed Symmetry Cases already corrected by Dick Marsh et al.
Recent Example of Missed Symmetry in J.A.C.S (2002) 124,

14. ADDSYM REPORT 2003/1
(25 out of 466)
>
>

15. J.A.C.S. 124 (2002) 9052
Communications

17. IUCR CHECKCIF ALERTS

18. NEWSYM Companion to ADDSYM Analysis
Structure factors calculated from current cell, symmetry and coordinate info.
Determination of the Space Group from the systematic absences in F(calc)
Extinctions in F(calc) may differ from those in F(obs) due to poor data.

21. QUATERNION FIT
In many cases, an automatic molecule fit can be performed
A) Identical atom numbering
B) Sufficient Unique Atoms
C) Manual picking of a few atom pairs

23. QUATERNION FIT

24. Cg Cg

25. STRUCTURE VALIDATION
Single crystal structure validation addresses three important questions:
1 – Is the reported information complete?
2 – What is the quality of the analysis?
3 – Is the Structure Correct?

26. HOT !

27. NOT SO HOT AFTER ALL !!

29.  

30. IUCR-CHECKCIF IUCR-TESTS: MISSING DATA, PROPER PROCEDURE, QUALITY
PLATON TESTS:
SYMMETRY, GEOMETRY, DISPLACEMENT PARAMETERS
ALERT LEVELS:
ALERT A - SERIOUS PROBLEM
ALERT B - POTENTIALLY SERIOUS PROBLEM
ALERT C - CHECK & EXPLAIN

31. Problems Addressed by PLATON
Missed Higher Space Group Symmetry
Solvent Accessible Voids in the Structure
Unusual Displacement Parameters
Hirshfeld Rigid Bond test
Miss-assigned Atom Type
Population/Occupancy Parameters
Mono Coordinated/Bonded Metals
Isolated Atoms

32. Problems Addressed by PLATON
Too Many Hydrogen Atoms on an Atom
Missing Hydrogen Atoms
Valence & Hybridization
Short Intra/Inter-Molecular Contacts
O-H without Acceptor
Unusual Bond Length/Angle
CH3 Moiety Geometry

33. Validation with PLATON
- Details:
Driven by the file CHECK.DEF with criteria, ALERT messages and advice.
Use: platon –u structure.cif
Result on file: structure.chk
Applicable on CIF’s and CCDC-FDAT
FCF-Valid: platon –V structure.cif

34. Example of Misplaced Hydrogen Atom

35. Two ALERTS related to the misplaced Hydrogen Atom

36. Unsatisfactory Hydrogen Bond Network

38. Satisfactory Hydrogen Bond Network with new H-position

43. SQUEEZE
Takes the contribution of disordered solvents into account by back-Fourier transformation of density found in the ‘solvent accessible volume’ outside the ordered part of the structure.
Filter: Input shelxl.res & shelxl.hkl
Output: ‘solvent free’ shelxl.hkl

47. SYSTEM S
Guided or Automatic Crystallographic Shell for Structure Determination from diffraction data to refined structure.
INPUT: HKL, CELL & CONTENT data
Interface to SHELX(S/L), DIRDIF,SIR97, POVRAY,RASTER3D, CSD etc.
Internal: PLATON Tools: Space Group Det, Abs.Cor., Graphics, ADDSYM etc.

48. Input for an Exec of System S
KappaCCD/DENZO: platon –s import.cif
Comp.hkl + comp.ins (= title,cell,sfac,unit,hklf 4) platon –s comp.ins
Comp.cif + comp.fcf (Acta): platon –s comp.cif
Default: suggestions for next step (can be overruled by the user)
Automatic Mode: add ‘nqa’:
platon –s comp.ins nqa

49. Finally Other features: Renaming of atoms, cif2res, asym-view
More Info: ‘
Right mouse clicks > help on menu item
DEMO