An Update on Current and New Structure Analysis Tools in PLATON

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An Update on Current and New Structure Analysis
Tools in PLATON
Ton Spek, Bijvoet Center for Biomolecular
Research, Utrecht University, The
Netherlands. ACA, Boston, Aug 1, 2012
Without Dikes Utrecht on Sea
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PLATON Updates
Similar to dikes, software requires maintenance
to keep up with current scientific needs, new
insights and changing standards PLATON is a
container of multiple software tools for chemical
crystallography The program is continuously
updated to keep up with Our own research
needs Ideas, bug reports and comments of
users The IUCr CheckCIF project Many
current changes are related to the anounced new
SHELXL2012 and SHELXT tools
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(No Transcript)
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f' and f'' and mu values
SHELXL and XL include (for all atom types)
proper values for f', f'' and mu exclusively for
the three wavelengths CuKa, MoKa and AgKa
Resonance values for other wavelengths
(synchrotron) have to be added manually with DISP
and SFAC records in the .ins. Also the wavelength
should be given with its actual value. If not,
CheckCIF will generate associated ALERTS PLATON
calculates suitable values following Brennan
Cowan (1962) Available instruction ANOM
wavelength (element)
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Resonance Scattering data calculated with PLATON
for lambda 1.8 Angstrom (following Brennan
Cowan)
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CIF FCF-Validation

• The SHELXL-2012 CIF will include the final .res
  and .hkl for additional documentation and future
  use, and implicitly includes info on twinning,
  constraint restraint details.
• FCF-Validation is now a standard part of the
  IUCr CheckCIF service. A listing file is created
  with a report on various issues
• - Variance analysis (similar to SHELXL) next
  example
• - Data set completeness beamstop reflections and
  outliers
• - Checks for unresolved twinning (TwinRotMat)
• - Checks on the value of the Flack parameter
  (Hooft y)
• - Residual density including density on atom
  sites

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Analysis Of Variance section
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The Disordered Solvent Problem

• Molecules of interest often co-crystallize (only)
  with the inclusion of a suitable solvent molecule
  in the lattice.
• Solvent molecules often fill voids in a structure
  with little interaction with the main molecule
  (disorder) and are often located on symmetry
  sites and with population less than 1.0
• Sometimes even the nature of the (mixture) of
  included solvent(s) is unclear.
• Refinement of a meaningful disorder model is
  preferable in cases of understood disorder (e.g.
  toluene disordered over an inversion centre)
• Refinement of cases of hopeless solvent disorder
  can be handled with the SQUEEZE method. The
  ordered part of the structure should have no
  unresolved issues and the data should be
  essentially complete to sin(theta/lambda) 0.6.
  There should be no charge balance problem.

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SQUEEZE

• Takes the contribution of disordered solvents to
  the calculated structure factors into account by
  back-Fourier transformation of density found in
  the solvent accessible volume outside the
  ordered part of the structure (iterated).
• Prototype and proof of principle implementation
  named BYPASS around the SHELX76 refinement tool.
  P. van der Sluis A.L. Spek, (1990). Acta
  Cryst. A46, 194-201
• Current implementation as PLATON/SQUEEZE around
  the SHELXL97 refinement tool. (Involving the
  solvent free .hkl file workaround, no proper twin
  handling)
• Soon SHELXL2012 now accepts fixed A B
  contributions of the solvent to the structure
  factor calculations thus eliminating the solvent
  free .hkl step.
• The new SHELXL2012 LIST 8 detwinned .fcf file
  will now allow the application of SQUEEZE for
  twins as well.

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THE MOLECULE THAT INVOKED THE BYPASS/SQUEEZE TOOL
Salazopyrin from DMF R 0.096
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Structure Modelling and Refinement Problem for
the Salazopyrin Structure
Difference Fourier map shows channels with
continuous density rather than maxima How to
handle and model this in the Refinement ? Our
solution SQUEEZE !
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Looking down the Infinite Channels in the
Salazopyrin Structure
The Problem Peak Search algorithms will not
always tell about the residual density. We need
special tools to detect voids in a modeled
structure.
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The
FIRST STEP OF SQUEEZE LOCATE SOLVENT ACCESSIBLE
VOID
Black areas indicate discrete model atom with van
der Waals radii assigned. The white area is the
solvent accessible volume
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Informal Theory of the SQUEEZE Procedure
I
M Ordered S Solvent
Iterate (Initially
Solvent Free ElectronCount
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SQUEEZE In the Complex Plane Trick needed to
refine with SHELXL97
Fc(solvent)
Fc(total)
Fc(model)
Fobs
Solvent Free Fobs
Black Split Fc into a discrete and solvent
contribution Red For SHELX97 refinement,
temporarily substract the recovered solvent
contribution from Fobs. (Reinstated after
convergence)
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• SQUEEZE Procedure with SHELXL97
• In this mode, the solvent contribution to the
  observed data is temporarily removed during the
  SHELXL refinement.
• 1 Standard name.ins/res name.hkl refinement to
  convergence shelxl name
• 2 Run PLATON/SQUEEZE as platon -q name.res with
  relevant results on name-sr.ins ( name.res),
  name-sr.hkl ( solvent free Fobs), name-sr.sqf (
  CIF info) name.lis
• Note This is difference map iteration and
  not refinement
• 3 Continue refinement to completion shelxl
  name-sr
• 4 Run PLATON as platon name-sr.res with the
  CalcFCF-sq menu tool to create a final CIF FCF
  (that again includes the original I(obs))

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SQUEEZE Procedure with SHELXL2012
In this more elegant mode, the observed Fobs data
remain untouched
1 Refine ordered model with name.ins ( ACTA)
and name.hkl as shelxl2012 name to convergence
gt name.cif name.fcf 2 Run SQUEEZE as platon
-q name.cif. The relevant output files are
name.lis, name_shelxl.ins ( name.res),
name_shelxl.hkl ( name.hkl), name_shelxl.fab
name-sr.sqf. 3 ADD the instruction 'ABIN' to
name_shelxl.ins 4 Refine as shelxl2012
name_shelxl (in the presence of name_shelxl_ins,
name_shelxl.hkl name_shelxl.fab) 5 Append the
'name-sr.sqf' file to the final name_shelxl.cif
to archive the details of the SQUEEZE run
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Refined structure without disordered solvent
(THF) contribution R 0.067, wR2 0.236, S
1.722 Rho(min) -0.49, Rho(max) 3.96
Refined structure (with SHELXL2012) After
SQUEEZE R 0.030, wR2 0.076, S
1.011 Rho(min) -0.35, Rho(max) 0.48
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SQUEEZE Procedure with SHELXL2012 and Twinning

• The SQUEEZE algorithm is based on the analysis
  of an untwinned difference map.
• SHELXL2012 can produce a 'type 8' style .fcf with
  detwinned data.
• This will provide a pathway to apply SQUEEZE to
  twinned structures
• However it is likely that the detwinning
  operation has to be recycled
• There is no experience yet

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Thanks !

• Thanks to all who have send me bug reports and
  useful suggestions
• And
• George Sheldrick for the new SHELX(T/2012)

PLATON runs from a terminal window under LINUX
and MAC-OSX And MS-Windows Louis Farrugia
MS-Windows GUI