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
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,
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.
25 STRUCTURE VALIDATIONSingle 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?
30 IUCR-CHECKCIF IUCR-TESTS: MISSING DATA, PROPER PROCEDURE, QUALITY PLATON TESTS:SYMMETRY, GEOMETRY, DISPLACEMENT PARAMETERSALERT LEVELS:ALERT A - SERIOUS PROBLEMALERT B - POTENTIALLY SERIOUS PROBLEMALERT C - CHECK & EXPLAIN
31 Problems Addressed by PLATON Missed Higher Space Group SymmetrySolvent Accessible Voids in the StructureUnusual Displacement ParametersHirshfeld Rigid Bond testMiss-assigned Atom TypePopulation/Occupancy ParametersMono Coordinated/Bonded MetalsIsolated Atoms
32 Problems Addressed by PLATON Too Many Hydrogen Atoms on an AtomMissing Hydrogen AtomsValence & HybridizationShort Intra/Inter-Molecular ContactsO-H without AcceptorUnusual Bond Length/AngleCH3 Moiety Geometry
33 Validation with PLATON - Details:Driven by the file CHECK.DEF with criteria, ALERT messages and advice.Use: platon –u structure.cifResult on file: structure.chkApplicable on CIF’s and CCDC-FDATFCF-Valid: platon –V structure.cif
43 SQUEEZETakes 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.hklOutput: ‘solvent free’ shelxl.hkl
47 SYSTEM SGuided or Automatic Crystallographic Shell for Structure Determination from diffraction data to refined structure.INPUT: HKL, CELL & CONTENT dataInterface 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.cifComp.hkl + comp.ins (= title,cell,sfac,unit,hklf 4) platon –s comp.insComp.cif + comp.fcf (Acta): platon –s comp.cifDefault: 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 itemDEMO