PLATON%20TUTORIAL

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PLATON TUTORIAL

• A.L.Spek,
• National Single Crystal Service Facility,
• Utrecht, The Netherlands.

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Who Are We ?

• We, a small group of 3 to 4 people run a National
  Single Crystal Service in the Netherlands since
  1971 (Utrecht University).
• (Bruker)Nonius KappaCCD on Rotating Anode
  Oxford LNT UNIX/LINUX Computers.
• Over 3000 structures studied so far, about 1800
  published in over 1100 papers.
• Mainly organometallic and coordination chemistry
• Main Software P.D. SHELX PLATON
• Co-Editor Acta Cryst. C (gt 850 papers handled)

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Tutorial Program

• 1 PLATON Overview Presentation
• 2 Life PLATON Demonstration (Linux)
• 3 Hands-on Exercises (MS-WINDOWS)
• 4 Lecture on Structure Validation

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What is PLATON

• A Multipurpose Crystallographic Tool.
• Developed in a Single Xtal Service Environment.
• Compatible with and Complementary to the Public
  Domain SHELX Bruker-AXS SHELXTL Software.
• Public domain (I.e. free-of-charge for
  academics, License Fee for For Profit
  Organizations).
• Available on UNIX/LINUX, MS-Windows MAC-OSX
  Platforms.

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Multipurpose Crystallographic Tool

• Automatic Geometry Analysis Listing.
• Molecular Graphics (PLUTON, ORTEP, Contour)
• Absorption Correction Tools(MULABS,TOMPA)
• ADDSYM - Check for Missed Symmetry.
• SQUEEZE Disordered Solvent Handling.
• Generation of Powder Patterns.
• Structure Validation (part of IUCr CHECKCIF).
• Analysis of Fo/Fc data including Bijvoet Pairs.
• System-S, Automated Structure Determination.
• Etc.

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EXAMPLE

• Input Shelx Style sucrose.res
• (Alternatively .cif,.pdb,.fdat,.spf style)
• Invoke PLATON (UNIX platon sucrose.res)
• Opening Menu (4 areas)
• Automatic ORTEP style PLOT
• Automatic PLUTON style PLOT
• Automatic NEWMAN PLOTS
• Simulated Powder Pattern
• H-Bond Table

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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
• NEWMAN PLOTS
• Simulated Powder Pattern
• H-Bond Table

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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
• NEWMAN Plots
• Simulated Powder Pattern
• H-Bond Table

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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
• NEWMAN Plots
• Simulated Powder Pattern
• H-Bond Table

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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
• NEWMAN Plots
• Simulated Powder Pattern
• H-Bond Table

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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
• NEWMAN Plots
• Simulated Powder Pattern
• H-Bond Table

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CALC ALL GEOMETRY LISTING

• With CALC ALL an exhaustive listing of derived
  intra-, inter- and coordination geometry etc. is
  produced.
• Two identical files are produced. .lis and
  lps. The first is lineprinter style, the latter
  is suitable for either a postscript printer or
  inspection with ghostview.
• We routinely provide this listing to the client
  along with an ORTEP.

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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)
gt

gt
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J.A.C.S. 124 (2002) 9052
Communications
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IUCR CHECKCIF ALERTS
Data From Supplementary Material
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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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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.
• Button VALIDATION on PLATON MAIN Menu
• Use platon u structure.cif
• Result on file structure.chk
• Applicable on CIFs 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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ARU-Definition

• Molecules (or unique asymmetric parts of a
  molecule) are assigned in PLATON an ARU value.
• npqr.s where n symmetry number and
• pqr translations and s the residue
• e.g. 2655.02
• Used to address symmetry related molecules in
  packing diagrams and intermolecular contacts.

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Solvent Accessible Voids

• A typical crystal structure has only 65 of the
  available space filled.
• The remainder volume is in voids in-between atoms
  (to small to accommodate an H-atom)
• Solvent accessible voids defined are regions in
  the structure that can accommodate at least a
  sphere with radius 1.2 Angstrom without
  intersecting with any of the van der Waals
  spheres assigned to each atom in the structure.

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DEFINE SOLVENT ACCESSIBLE VOID
STEP 1 EXCLUDE VOLUME INSIDE THE VAN DER
WAALS SPHERE
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DEFINE SOLVENT ACCESSIBLE VOID
STEP 2 EXCLUDE AN ACCESS RADIAL VOLUME TO
FIND THE LOCATION OF ATOMS WITH THEIR CENTRE AT
LEAST 1.2 ANGSTROM AWAY
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DEFINE SOLVENT ACCESSIBLE VOID
STEP 3 EXTEND INNER VOLUME WITH POINTS
WITHIN 1.2 ANGSTROM FROM ITS OUTER BOUNDS
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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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SQUEEZE PROCEDURE

• Refine structure including H-atoms
• Use .res and .hkl for the SQUEEZE calculation
• Continue refinement using the reflection file
  produced by SQUEEZE
• Calculate a final .fcf using the latest .res and
  .hkl (from SQUEEZE) using PLATON/FCF
• Append the .fsq file to the final .cif for
  publication.

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Twinning

• Twinning results in overlap of reflections with
  different hkl
• Twinning can be detected during the data
  collection experiment
• Cases of (Pseudo) Merohedral twinning are
  generally detected during the structure
  determination

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TWINNING - SYMPTOMS

• Spots that do not fit in the proposed lattice
• Strange extinctions
• Laue symmetry higher than consistent with the
  systematic extinctions.
• E-statistics
• Unexpected high R-value
• Ghost peaks in the difference map
• A Significant of reflections with Fobs gtgt Fcalc

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TWIN DETECTION

• SOFTWARE ROTAX PLATON/TWINROTMAT
• ANALYSIS BASED ON (CIF ) FCF FILES
• PROPOSALS FOR TWIN-OPERATION

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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, SIR2002,
  POVRAY,RASTER3D etc.
• Internal PLATON Tools Space Group Det,
  Abs.Cor., Graphics, ADDSYM etc.

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Input for an Exec of System S

• System S is available for LINUX only
• 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 gt help on menu item
• DEMO