PLATON TUTORIAL

A.L.Spek,

National Single Crystal Service Facility,

Utrecht, The Netherlands.

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

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.

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

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

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?

HOT !

NOT SO HOT AFTER ALL !!

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.

- 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

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

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.

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

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