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PLATON TUTORIAL

PLATON TUTORIAL. A.L.Spek, National Single Crystal Service Facility, Utrecht, The Netherlands. What is PLATON. A Multipurpose Crystallographic Tool Compatible with and Complementary to P.D. SHELX & Bruker-AXS SHELXTL

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PLATON TUTORIAL

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  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

  5. 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) 124,11846-11847

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

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

  8. IUCR CHECKCIF ALERTS

  9. 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.

  10. 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

  11. QUATERNION FIT

  12. Cg1 0.946 0.234 0.592 Cg2 0.441 0.253 0.581

  13. 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?

  14. HOT !

  15. NOT SO HOT AFTER ALL !!

  17. 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

  18. 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

  19. 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

  20. Validation with PLATON - Details: www.cryst.chem.uu.nl/platon • 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

  21. Example of Misplaced Hydrogen Atom

  22. Two ALERTS related to the misplaced Hydrogen Atom

  23. Unsatisfactory Hydrogen Bond Network

  24. Satisfactory Hydrogen Bond Network with new H-position

  25. 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

  26. 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.

  27. 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

  28. Finally • Other features: • Renaming of atoms, cif2res, asym-view • More Info: • ‘www.cryst.chem.uu.nl/platon’ • Right mouse clicks > help on menu item • DEMO

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