platon tutorial a.l.spek, national single crystal service facility, utrecht, the netherlands
TRANSCRIPT
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PLATON TUTORIAL
A.L.Spek,
National Single Crystal Service Facility,
Utrecht, The Netherlands.
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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
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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.
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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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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
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ADDSYM REPORT 2003/1
>
>
(25 out of 466)
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J.A.C.S. 124 (2002) 9052
Communications
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IUCR CHECKCIF ALERTS
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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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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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QUATERNION FIT
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Cg1 0.946 0.234 0.592
Cg2 0.441 0.253 0.581
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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?
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HOT !
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NOT SO HOT AFTER ALL !!
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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
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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
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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
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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
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Example of Misplaced Hydrogen Atom
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Two ALERTS related to the misplaced Hydrogen Atom
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Unsatisfactory Hydrogen Bond Network
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Satisfactory Hydrogen Bond Network with new H-position
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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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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.
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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
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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