PLATON/CheckCIF Issues
Ton Spek
Utrecht University
The Netherlands
Bruker User Meeting
UCSD, La Jolla,
March 22-24, 2012
Selected Validation Issues
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Structure validation is an ongoing project due to
changes in procedures, software and hardware
Many validation criteria are empirical and might
need a theoretical background.
Proper correction for absorption was
considered very important in the 1990's and is
currently a lesser issue (The SADABS effect)
Absolute structure determination of light atom
structure has changed in view of the supposedly
more sensitive Hooft y and Parsons z
parameters as compared with the Flack x
parameter
Cell Parameters and s.u.'s
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Unit cell parameters determined with serial
detectors were generally based on the setting
angles of 25 reflections and generally
produced realistic looking s.u.'s.
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Currently, cell dimensions are determined from
the detector positions of many thousands of
reflections. Their s.u.'s are often unrealistically
small.
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It is probably best not to artificially increase
the s.u.'s in a report with a guessed factor but
leave that to the user of the data
Unit cell Volume s.u.
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SHELXL calculates the volume s.u. assuming
3 independent parameters. Angle s.u.'s are
not taken into account (CheckCIF does)
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PLATON/CheckCIF calculates the more
appropriate cubic crystal cell volume s.u. as
3a2 x sigma(a) which often leads to an ALERT
when calculated with SHELXL.
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Reporting the same s.u. for a,b and c can be
confusing
Connected Sets of Atoms
- Atoms should be transformed by symmetry
operations into a suitable connected set
- Centers of gravity of the species of the
asymmetric unit should generally lie within the
bounds of the unit cell
- Exceptions are small molecules (e.g. H2O) that
should be close to the main species in order to
avoid unnecessary symmetry operations in Hbond tables
This is an example of bad practice
Symmetry
- PLATON accepts the specification of the
spacegroup symmetry in various formats:
a) Explicit: SYMM and LATT records
b) Hermann-Mauguin symbol (PLATON knows
about many variations beyond the standard 230)
c) Hall Symbol (Explicit and eventually used to
generate the set of symmetry operations used)
- a), b) and c) info in the CIF is cross checked
n_hkl Symmetry Codes
- PLATON adheres to the set of symmetry codes
consistent with those in the International Tables
(i.e. produced from the generators implicit in the
Hall symbol of the space group at hand).
- SHELXL allows for a more flexible specification
and ordering of non-centering and inversion
operations. Translation components can be
negative (e.g -1/2).
- The validation software takes this difference into
account for the n_hkl symmetry codes in e.g. Hbonding geometry: H-bond tables in PLATON
list both the 'PLATON' and 'SHELXL' codes.
Shelxl s.o.f. versus CIF occupancy
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The SHELXL definition of occupancy in the .res and
the CIF definition of occupancy are different
This often results in confusion, wrong formula and
related ALERTS
The difference shows up for atoms on special
positions
SHELXL generally handles (but not always) this issue
when creating a .cif
Unfortunately there exists an inconsistency related to
the specification of the multiplicity as well (see below)
SHELXL definition of s.o.f.
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.. the site occupation factor is normally given as
11 (i.e. fixed at 1). The site occupation factor for
an atom in a special position should be
multiplied by the multiplicity of that position (as
given in International Tables, Volume A) and
devided by the multiplicity of the general
position for that space group.
.. an atom on a fourfold axes example will
usually have s.o.f. = 10.25 .. and a fully
occupied atom on an inversion center s.o.f. =
10.5
CIF Definition of Occupancy
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_atom_site_occupancy
… the fraction of the atom type present at this site …
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_atom_site_symmetry_multiplicity
.. the multiplicity of a site due to space-group symmetry as
given in International Tables for Crystallography Vol. A
(2002) .. the permitted range is 1 -> 192 ..
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Thus 'multiplicity' for atom on fourfold axis in P4 ??
SHELXL CIF .. 1.0 4 (sometimes 0.25 1)
Officially …..... 1.0 1 ??
Other occupancy Issues
- SHELXL s.o.f.'s should be given with sufficient
number of decimals for atoms on special
positions. Thus 0.33333 and 0.66667 rather
than 0.33 and 0.666
- The rounding of refined occupation numbers
may lead to non-unity sums for the total
occupancy of a chemically relevant atom,
leading to non-integer atom counts in the
formula.
Disorder
- PLATON by default automatically detects
disorder fragments on the basis of occupation
numbers: Bonds are assumed either between a
fully occupied atom and a partially occupied site
or between to atoms with the same population.
Might fail in exactly 50:50% disorder cases
- SHELXL introduced the 'PART' concept many
years after the the design of PLATON.
Implementation of the PART concept in PLATON
is now underway.
Formula & Z
- The Moiety Formula should be consistent with
the reported Z value. There should be generally
no problem with one species only in a general
position (Z = general position multiplicity)
- The proper choice of Z in the case of multiple
species in the asymmetric unit (and their order)
is likely best dictated by the underlying
chemistry.
Standard Setting
- Reporting a structure in a standard setting can
often make the search for similar structures
easier.
- Available rules: Niggli reduced, a<b<c etc.
- Hot issues: P21/c versus P21/n (closer to 90 deg)
- For (in particular inorganic compounds)
'Structure Tidy'
Resolution of the Dataset
- Acta Cryst. prefers a dataset that is essentially
complete up to sin(theta)/lambda = 0.6
- Exceptions can be beamstop reflections and hardware
constraints such as a high pressure cell
- Generally all observed reflections above
sin(theta)/lambda = 0.6 should be retained
- The values for the data names for completeness and
theta_full can be changed from the values given in the
CIF by SHELXL to satisfy the first condition.
- Missing cusps of data can usually be avoided
Do Not remove by default
data beyond
sin(theta)/lambda = 0.6
Absolute Structure
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The reported Flack parameter value is
checked against the value of the Hooft
parameter.
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The Hooft parameter requires a high Bijvoet
pair coverage
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The Flack parameter is best determined with
the BASF/TWIN instruction (without matrix !)
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R & S configuration assignments are
suggested (unfortunately, the algorithm used
may error for complicated ring systems)
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.
– PLATON offers suitable values following Brennan &
Cowan (1962)
– CheckCIF compaires the values in the .cif with the
expected values for the reported wavelength.
Resonance Scattering data calculated with PLATON for lambda =
1.8 Angstrom (following Brennan & Cowan)
Weight Optimization
– SHELXL provides two parameters for automatic
reflection weight optimisation ( a & b). The S
value is expected to converge to a value close
to zero.
– Large values generally indicate model or data
problems. Examples are twinning, wrong
symmetry, wrong atom type assignments,
unresolved disorder and solvent.
Weight Optimization
– SHELXL provides two parameters for automatic
reflection weight optimisation ( a & b). The S
value is expected to converge to a value close
to zero.
– Large values generally indicate model or data
problems. Examples are twinning, wrong
symmetry, wrong atom type assignments,
unresolved disorder and solvent.
Hydrogen Atom Treatment
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The parameters of hydrogen atoms on hetero
atoms are best refined to prove their validity.
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Other hydrogen atoms are generally best
taken into account in the riding mode to
secure a good data over parameter ratio.
Missed or Pseudo symmetry
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The ADDSYM routine in PLATON analyses a
coordinate set for additional symmetry.
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The tolerances are set on values intended to
catch both missed and (interesting) pseudo
symmetry.
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Corresponding ALERTS should be
investigated and either corrected or discussed
Difference Electron Density Map
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The difference electron density map should be
essentially featureless
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Significant positive or negative density on atom positions
may indicate wrong atom type assignment or inadequate
correction for absorption.
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Another cause may be the improper use of the SHELXL
'DAMP 0' for a non-converged refinement.
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Disorder in solvent regions may not show up in a peak
list.
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Seriously in error strong reflections show up as positive
and negative bands.
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Density peaks in chemically unreasonable positions may
indicate twinning.
Voids and SQUEEZE
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Generally, crystal structures contain no
significant solvent accessible voids. Most will
collapse when their solvent of crystallization
evaporates
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The SQUEEZE tool may be used to show
either that there is no residual density in a
VOID or to correct for its contribution
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In the latter case, info should be added to the
CIF and FCF
Automated Twinning Detection
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TwinRotMat attempts to report on twinning
based on the data in the .fcf.
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The related ALERTS may either confirm cases
of twinning that have been addressed in the
structure refinement or cases of missed
twinning.
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Unfortunately no official datanames to report
on twinning in the CIF are available yet.
Hirshfeld Rigid Bond Test
– CheckCIF uses the Hirshfeld Rigid Bond test
outside its originally intended context (i.e. light
atom structures).
– Large values may indicate misassigned atom
types or disorder.
– ALERT levels are to be a function of the
associated chemistry (e.g. M..C=O), data quality
and resolution.
Unusual Molecular Geometry
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Unusual hybridization
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Unusual bond distances
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Phenyl ring with a large difference of the
average bond distance from the expected
1.395 (due to wrong cell dimensions ?)
Short Intermolecular Contacts
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Short intermolecular contacts should be
investigated. They can indicate
– Missing Hydrogen atom in a hydrogen bond
– wrong structure / wrong H-atom positions
– improper description of a disorder
– improperly modelled solvent
– Interesting contact to be discussed (e.g.
halogen-halogen)
Analysis of the Reflection Data
– The data names and cell dimensions in the CIF
and FCF should be identical.
– The CIF and FCF should be from the same
refinement.
– Missing low order reflection data along with their
expected values are reported
– Outliers with large Fo/Fc differences are
reported
– Checks for the consistency of CIF & FCF data
– Calculation of the 'non weight optimized S value
Residual Issues and Challenges
- SHELXL/CIF provided defaults should be
updated to their actual values.
- Validation of Powder, Charge Density and
Incommensurate structures still open for
development (experts needed)
- Avoid False positive and negative ALERTS
- Fabricated reflection data. Can we detect them ?
- Education – what is thye meaning of a particular
ALERT
- Should validation criteria be different for
References
A.L.Spek, J. Appl. Cryst. (2003). 36, 7-13.
A.L.Spek, Acta Cryst. D65, 148-155.