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PLATON TUTORIAL A.L.Spek, National Single Crystal Service Facility,

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Presentation on theme: "PLATON TUTORIAL A.L.Spek, National Single Crystal Service Facility,"— Presentation transcript:

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

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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,

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

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

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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.

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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

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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 !!

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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

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38 Satisfactory Hydrogen Bond Network with new H-position

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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

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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: ‘www.cryst.chem.uu.nl/platon’ Right mouse clicks > help on menu item DEMO


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