Transcript PLATON TUTORIAL - National Single Crystal X

PLATON, A Multipurpose
Crystallographic Tool
Ton Spek,
National Single Crystal Service
Facility,
Utrecht, The Netherlands.
What is PLATON
• A Multipurpose Crystallographic Tool.
• A Program Developed in, and Addressing the
needs of, a Single Crystal Service Environment.
• Compatible with and Complementary to the
Public Domain SHELX & Bruker-AXS
SHELXTL Software. (.res,.hkl,.cif,.fcf)
• ‘Semi Public domain’ (I.e. free-of-charge for
academics, but with a License Fee for For Profit
Organizations).
• Developed on UNIX/LINUX and available on
MS-Windows & MAC-OSX Platforms.
Multipurpose Crystallographic
Tool
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Automatic Geometry Analysis & Listing.
Molecular Graphics (ORTEP, PLUTON, Contour)
Absorption Correction Tools(MULABS,TOMPA)
ADDSYM - Check for Missed Symmetry.
SQUEEZE – Disordered Solvent Handling.
Generation of Powder Patterns (Coordinates, hkl)
Structure Validation (part of IUCr CHECKCIF).
Analysis of Fo/Fc data including Bijvoet Pairs.
Analysis of (Pseudo) Merohedral Twinning.
System-S, Automated Structure Determination.
EXAMPLE
• Input Shelx Style: sucrose.res
• Alternatively:
.cif, .pdb, .fdat, .spf style files
• Invoke PLATON:
UNIX: platon sucrose.res
MS-Windows: via ‘Farrugia’ task menu
• Opening Menu (4 areas) 
EXAMPLE
• Input Shelx Style: sucrose.res
• (Alternatively: .cif,.pdb,.dat,.spf style)
• Automatic ORTEP style PLOT 
EXAMPLE
• Input Shelx Style: sucrose.res
• (Alternatively: .cif,.pdb,.dat,.spf style)
• Automatic PLUTON style PLOT 
EXAMPLE
• Input Shelx Style: sucrose.res
• (Alternatively: .cif,.pdb,.dat,.spf style)
• NEWMAN Plots 
EXAMPLE
• Input Shelx Style: sucrose.res
• (Alternatively: .cif,.pdb,.dat,.spf style)
• Simulated Powder Pattern (hkl or coord)
• from coordinates 
Intra-molecular Geometry
• Atom list sort.
• Detection of residues (connected set) and
derivation of the Moiety formula, Z and Z’.
• Bond distances, Bond Angles, Torsion Angles.
• Automatic ring search,automatic seach of planar
parts in the structure
Intra-Molecular (Continued)
• Determination of the hybridization, R/S
assignments and ‘topology numbers’.
• Listing of the plane-plane and bond-plane
angles.
• Ring puckering analysis (Cremer & Pople)
Example 
Inter-Molecular
• Hydrogen Bonds (linear, bi- and trifurcated)
• Automatic analysis in terms of 1, 2 and 3-D
networks (aggregates or cooperative)
• Search for pi-pi and C-H..pi interactions
• Example H-Bond Table 
CALC ALL GEOMETRY
LISTING
• With CALC ALL an exhaustive listing of derived
intra-, inter- and coordination geometry etc. is
produced, including a structure validation report.
• Two ‘content 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 exhaustive listing to the
chemist/client along with an ORTEP.
PLATON/ADDSYM ANALYSIS
• Example of a missed symmetry case from
the CSD 
BAMYEU
Dalton Trans
2003,134-140
Cc
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.
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
QUATERNION FIT
Cg1 0.946 0.234 0.592
Cg2 0.441 0.253 0.581
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?
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
Problems Addressed by PLATON
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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
Problems Addressed by PLATON
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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
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 CIF’s and CCDC-FDAT
- FCF-Valid: platon –V structure.cif
Example of Misplaced Hydrogen Atom
Two ALERTS related to the misplaced Hydrogen Atom
Unsatisfactory Hydrogen Bond Network
Satisfactory Hydrogen Bond Network with new H-position
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 are defined as 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.
DEFINE SOLVENT ACCESSIBLE VOID
STEP #1 – EXCLUDE VOLUME INSIDE THE
VAN DER WAALS SPHERE
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
DEFINE SOLVENT ACCESSIBLE VOID
STEP # 3 – EXTEND INNER VOLUME WITH POINTS WITHIN
1.2 ANGSTROM FROM ITS OUTER BOUNDS
Cg
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
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.
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
(Pseudo)Merohedral Twinning
• Options to handle twinning in L.S. refinement available in
SHELXL, CRYSTALS etc.
• Problem: Determination of the Twin Law that is in effect.
• Partial solution: coset decomposition, try all possibilities
(I.e. all symmetry operations of the lattice but not of the
structure)
• ROTAX (S.Parson et al. (2002) J. Appl. Cryst., 35, 168.
(Based on the analysis of poorly fitting reflections of the
type F(obs) >> F(calc) )
• TwinRotMat Automatic Twinning Analysis as
implemented in PLATON (Based on a similar analysis but
implemented differently)
Example
• Structure refined to R= 20% in P-3
• Run TwinRotMat on CIF/FCF
• Result: Twinlaw with estimate of the
twinning fraction and drop in R-value
Absolute Structure
• The absolute structure of a compound is
normally determined with the refinement of
the Flack parameter.
• The value of the Flack parameter can be
inconclusive in view of a high su.
• A detailed scatter-plot may be more
conclusive.
BIJVOET PAIR
SCATTER PLOT
System S
• Automatic structure determination
(Space group determination, solution,
refinement, analysis)
• Build-in in PLATON (Unix only)
• Calls external programs including itself for
various functions.
• Program runs in either guided or noquestions-asked mode
SYSTEM S
• INPUT: HKL, CELL & CONTENT data
• Interface to SHELX(S/L), DIRDIF,SIR97,
SIR2002, POVRAY,RASTER3D etc.
• Internal: PLATON Tools: Space Group Det,
Absorption Correction, Graphics,
Validation, ADDSYM etc.
• Platon –s compound.ins nqa
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Other features:
Structure Tidy (CIF input)
Bond Valence
Renaming of atoms, cif2res, asym-view
More Info:
‘www.cryst.chem.uu.nl/platon’
Right mouse clicks > help on menu item
Thanks
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Thanks to the users for their:
Complaints
Bug reports (‘undocumented features ..)
Suggestions
And you for your attention