Transcript PLATON TUTORIAL - National Single Crystal X

PLATON TUTORIAL
A.L.Spek,
National Single Crystal Service
Facility,
Utrecht, The Netherlands.
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 (> 850 papers handled)
Tutorial Program
• 1 PLATON Overview Presentation
• 2 Life PLATON Demonstration (Linux)
• 3 Hands-on Exercises (MS-WINDOWS)
• 4 Lecture on Structure Validation
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.
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…….
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
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
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
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
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
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
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.
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
ADDSYM REPORT 2003/1
(25 out of 466)
>
>
J.A.C.S. 124 (2002) 9052
Communications
IUCR CHECKCIF ALERTS
Data From Supplementary Material
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
-
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
-
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
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.
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.
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
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
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 >> Fcalc
TWIN DETECTION
• SOFTWARE: ROTAX &
PLATON/TWINROTMAT
• ANALYSIS BASED ON (CIF &) FCF
FILES
• PROPOSALS FOR TWIN-OPERATION
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.
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
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