CRYSTALS Enhancements: Asymmetric Restraints

Sep 212012
 

J. Appl. Cryst. (2012). 45, 1057–1060. [ doi:10.1107/S0021889812035790 ]

The traditional Waser distance restraint, the rigid-bond restraint and atomic displacement parameter (ADP) similarity restraints have an equal influence on both atoms involved in the restraint. This may be inappropriate in cases where it can reasonably be expected that the precision of the determination of the positional parameters and ADPs is not equal, e.g. towards the extremities of a librating structure or where one atom is a significantly stronger scatterer than the other. In these cases, the traditional restraint feeds information from the poorly defined atom to the better defined atom, with the possibility that its characteristics become degraded. The modified restraint described here feeds information from the better defined atom to the more poorly defined atom with minimal feedback.

Electronic reprints

Publisher’s copy

 

Summer Conferences – ACA Annual Meeting 2012, ECM 27 and Aperiodic 2012

Aug 102012
 

Summer is conference season and the members of Chem. Cryst. have been on the road to the ACA in Boston and the ECM in Bergen.  In September, Kirsten will also be attending the 7th International Conference on Aperiodic Crystals, to be hosted in Cairns, Australia.  Contributions include:

David J. Watkin, Richard I. Cooper & Anna Collins
Z’>1 Structures. Just a Nuisance or Something More Interesting? (ACA; Oral presentation)

Karim J. Sutton, Richard I. Cooper, Kirsten E. Christensen, Amber L. Thompson, David R. Allan & Sarah A. Barnett
Exploiting the Tunable Wavelength Capabilities of Synchrotron Radiation for Small Molecule Single Crystal X-ray Crystallography (ACA; Prize winning oral presentation)

Richard I. Cooper
CRYSTALS: Teaching an Old Dog New Tricks (ACA; Oral presentation)

Amber L. Thompson
When Small Molecules Get Large – A Journey into the Unknown (ECM; Oral presentation)

Anthony Linden & Amber L. Thompson
Hot topics and Structures in Molecular Chemistry (ECM; Microsymposium)

Kirsten E. Christensen & Amber L. Thompson
New Challenges in Chemical Crystallography (Aperiodic; Oral presentation)

 

Along the bryggen in Bergen

Along the bryggen in Bergen

In Bergen

In Bergen

Something smells a little fishy

Something smells a little fishy

A BIG fishy!

A BIG fishy!

It really *IS* that expensive in Norway!

It really *IS* that expensive in Norway!

Albert Einstein or Edvard Greig?

Albert Einstein or Edvard Greig?

Norwegian Humour

Norwegian Humour

 

Applications of Leverage Analysis in Structure Refinement

Apr 302012
 

J Appl. Cryst. (2012), 45, 417-429. [ doi:10.1107/S0021889812015191 ]

Leverages measure the influence that observations (intensity data and restraints) have on the fit obtained in crystal structure refinement. Further analysis enables the influence that observations have on specific parameters to be measured. The results of leverage analyses are discussed in the context of the amino acid alanine and an incomplete high-pressure data set of the complex bis(salicylaldoximato)copper(II). Leverage analysis can reveal situations where weak data are influential and allows an assessment of the influence of restraints. Analysis of the high-pressure refinement of the copper complex shows that the influence of the highest-leverage intensity observations increases when completeness is reduced, but low leverages stay low. The influence of restraints, notably those applying the Hirshfeld rigid-bond criterion, also increases dramatically. In alanine the precision of the Flack parameter is determined by medium-resolution data with moderate intensities. The results of a leverage analysis can be incorporated into a weighting scheme designed to optimize the precision of a selected parameter. This was applied to absolute structure refinement of light-atom crystal structures. The standard uncertainty of the Flack parameter could be reduced to around 0.1 even for a hydrocarbon.

Electronic reprints

Publisher’s copy

CRYSTALS Enhancements: Absolute Structure Determination

Sep 132011
 

J. Appl. Cryst.  (2011), 44, 1017-1022.    [ doi:10.1107/S0021889811034066 ]

A summary of the features for investigating absolute structure available in the crystallographic refinement program CRYSTALS is presented, together with the results of analyses of 150 light-atom structures collected with molybdenum radiation carried out with these tools. The results confirm that the Flack and Hooft parameters are strongly indicative, even when the standard uncertainties are large compared to the thresholds recommended by Flack & Bernardinelli [J. Appl. Cryst. (2000), 33, 1143–1148].

Electronic reprints

  • Oxford University Research Archive [direct pdf]

Publisher’s copy

CRYSTALS v14.23

May 122011
 

CRYSTALS v14.23c installer is available to download for the Windows platfom.

[Update - patched version 1423c released 27 May, fixes format problem with tiny weights in FCF, CIF input bug]

Selected highlights:

  • Added bond colouring to indicate either element type, or disordered part
  • Improved robustness of weighting scheme 17 (Shelx weights)
  • Output observation weights in FCF CIF
  • Allow omission of Friedel pairs of reflections from Absolute Configuration plots.
  • Fixed crash on ‘Select All’ atoms for large structures.
  • Fixed Hide/Show H button on toolbar.

CRYSTALS 14.21

Apr 212011
 

CRYSTALS v14.21 installer is available to download for the Windows platfom.

Selected highlights:

  • Constraints (List 12), restraints (List 16) and manually omitted reflections (List 28) are appended to the CIF for easy reference.
  • Punch for list 1 is now possible.
  • Included slant 2Fo-Fc maps on the menu.
  • Fixed 2 bugs in #Perhydro: phenyl rings now work again and addition of H to disordered components is fixed.
  • New list 9 stores parameter standard uncertainties from last cycle of least squares.
  • New script for reading general CIFs from diffractometers.
  • New script for centering structures in cells.
  • Reduced number of questions during reading back of Superflip solutions.
  • New script for editing f’ and f”.

 

Practical Applications of Averages and Differences of Friedel Opposites

Dec 072010
 

Acta Cryst. (2011), A67, 21-34.    [ doi:10.1107/S010876731004287X ]

The practical use of the average and difference intensities of Friedel opposites at different stages of structure analysis has been investigated. It is shown how these values may be properly and practically used at the stage of space-group determination. At the stage of least-squares refinement, it is shown that increasing the weight of the difference intensities does not improve their fit to the model. The correct form of the coefficients for a difference electron-density calculation is given. In the process of structure validation, it is further shown that plots of the observed and model difference intensities provide an objective method to evaluate the fit of the data to the model and to reveal insufficiencies in the intensity measurements. As a further tool for the validation of structure determinations, the use of the Patterson functions of the average and difference intensities has been investigated and their clear advantage demonstrated.

Electronic reprints

Publisher’s copy

CRYSTALS 14.11

Jul 312010
 

CRYSTALS v14.11 is available as a beta-test.

Many small changes in Regularise Replace thanks to a CRYSTALS workshop in Toulouse organised by Carine Duhayon and Laure Vendier.

Cif generator now properly includes esds on refined hydrogen bonds, has incrreased figure-fields for cell parameters, and appends constraint and restraint information as _iucr_ data items at end of cif.

Improved scaling of difference Pattersons – see forthcoming paper by Flack, Sadki, Thompson & Watkin.

Absolute configuration routine (based on PLATON with Ton Spek’s permission) extended to provide more diagnostics and additional data to be re-input as absolute-structure strengthening restraints (see paper by Flack et al. above).

Error tracking for “USE” files has been improved.

Collaboration with Ernesto Mesto (Dipartimento Geomineralogico – Università degli Studi di Bari) uncovered over-sights in the original 1979 code, which lost contributions when a twin component fell onto a centring absence. Difference maps with twinned data now seem to reveal hydrogen atoms very reliably.

CRYSTALS Enhancements: Dealing with Hydrogen Atoms in Refinement

Jun 292010
 

J. Appl. Cryst. (2010), 43, 1100-1107.    [ doi:10.1107/S0021889810025598 ]

Because they scatter X-rays weakly, H atoms are often abused or neglected during structure refinement. The reasons why the H atoms should be included in the refinement and some of the consequences of mistreatment are discussed along with selected real examples demonstrating some of the features for hydrogen treatment that can be found in the software suite CRYSTALS.

Hydrogen addition in CRYSTALS

Hydrogen addition in CRYSTALS

Electronic reprints:

Publisher’s copy:

An Unusual Methylene Aziridine Refined in P21/c and the Nonstandard Setting P21/n

Nov 182009
 

Acta Cryst. (2009), C65, o635-o638.    [ doi:10.1107/S0108270109046952 ]

The unusual methylene aziridine 6-tert-butyl-3-oxa-2-thia-1-azabicyclo[5.1.0]oct-6-ene 2,2-dioxide, C9H15NO3S, was found to crystallize with two molecules in the asymmetric unit. The structure was solved in both the approximately orthogonal and the oblique settings of space group No. 14, viz. P21/n and P21/c, respectively. A comparison of these results clearly displayed an increase in the correlation between coordinates in the ac plane for the oblique cell. The increase in the corresponding covariances makes a significant contribution to the standard uncertainties of derived parameters, e.g. bond lengths. Since there is yet no CIF definition for the full variance-covariance matrix, there are clear advantages to reporting the structure in the nonstandard space-group setting.

Publisher’s copy: IUCr

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