Transcript An Update on Current and New Structure Analysis Tools in

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
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
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)
Resonance Scattering data calculated with PLATON for lambda =
1.8 Angstrom (following Brennan & Cowan)
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
Analysis
Of
Variance
section
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.
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.
THE MOLECULE THAT INVOKED THE BYPASS/SQUEEZE TOOL
Salazopyrin from DMF – R = 0.096
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 !
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.
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
Informal Theory of the SQUEEZE Procedure
M = Ordered
S = Solvent
I
Iterate (Initially
Solvent Free
ElectronCount
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)
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))
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 =>
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 & namesr.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
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
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
Thanks !
PLATON runs from a terminal window under LINUX and MAC-OSX
And MS-Windows + Louis Farrugia MS-Windows GUI
Thanks to all who have send me bug reports and
useful suggestions
And
George Sheldrick for the new SHELX(T/2012)