Richard Cooper

Aug 292018
 

The 31st European Crystallography Meeting was held in Oviedo, Spain from 22-26 August 2018.

During the meeting George Sackman presented a poster (MS10-P05) on recent neutron diffraction work with Richard Cooper and Alison EdwardsDisordered or not: A cautionary tale when inferring proton disorder solely from X-ray and computational data.

Richard Cooper gave a presentation (GI-MS47-O5) in the Saturday afternoon session How to… take your next steps in crystallography, based on experience of a career which despite including several areas of science and organisations rarely strayed outside the OX postcode.

On Sunday afternoon Amber Thompson presented (MS27-O5) Adventures in modulation: derivatives of Barluenga’s reagent, including work from Lewis Morgan, Yejin Kim, Emma McKinley, Jack Blandy, Claire Murray and Kirsten Christensen, in the session Quasicrystals: theory and
experiment.

Prior to the meeting, Richard Cooper was a tutor at the ECA Crystallographic Computing School in Mieres, organised by the ECA SIG 9 and gave a lecture on Programming Crystallographic Symmetry.

Jul 182018
 

The CRYSTALS v6999 installer for Windows 7/10 is now available.

Please report problems. The version number (6999) refers to a specific snapshot of the source code enabling us to better identify and fix bugs.

Key changes between 14.6720 and 14.6999
Added some trial shortcut keys to the menus. Ctrl-O: open file dialog, Ctrl-R: setup refinement, Alt-R: do refinement, Alt-S: refine scale, Alt-C: sfls/calc, Ctrl-H: hydrogen fourier, Ctrl-Y: cameron, Ctrl-W: wilson, Ctrl-F: fo vs fc, Ctrl-A: agreement analysis, Ctrl-R: rotax!
Added menus to the xeditorgl script so that Ctrl+S, Alt-F4 key combination works for save and exit.
Fix quoting of paths with spaces in SCRIPTS so that CRYSTALS can be installed in, and process data in, paths with spaces.
Removed default low angle cutoff in L28 – should be handled by instrument software.
Allow negative twin element scales. Setting negative scales back to zero was breaking twin element scale constraints.
Tool-help option (see Tools menu) shows quick explanatory text before carrying out immediate tasks from menus.
Punch of L30 implemented – all lists can now be punched!
Dialog and options for launching SHELXT (solve menu).
Fix weird bug that caused crash when importing structures containing cobalt and using Cu X-ray scattering factors.
New shelx2cry by Pascal used for .ins and .res conversion – much better conversion of standard SHELX syntax.
‘Sticky refine’ mode code improved and made user interface more intuitive.
Removed old shift rescaling code, it slowed convergence of some key parameters.
New leverage information output of restraints (#CHECK). Restraints with no leverage are pointless, while a leverage of ~1 indicates they dominate refined value of parameter of function of parameters.
Code to output leverage data (punch=numpy) during SFLS. Data in python format to allow user calculations to be added.

Jun 242018
 

Journal of Applied Crystallography, 2018, 51, 1059-1068. [ doi: 10.1107/S1600576718007100 ]

The implementation and use of a set of new displacement parameter restraints is described. Anisotropic displacement parameters account for a large proportion of the parameters in a crystallographic refinement, but very few restraints for conveniently controlling their values have been implemented in standard crystallographic refinement programs.

Jun 172018
 

The Great Wall of China (Huangyaguan section)Though it should be an off-year, the long-running biennial Zurich School of Crystallography visited the Health Science Platform of the University of Tianjin in June 2018 to teach a group of international researchers how to use single crystal X-ray crystallography.

Richard Cooper joined the Swiss delegation of tutors and gave lectures on space group determination and the use of Hirshfeld surfaces in crystal structure analysis.

Right: The Great Wall of China (Huangyaguan section): Lukas Palatinus and Hans-Beat Bürgi in the distance.

 

Nov 132017
 

The CRYSTALS v6720 installer is now available.

This update uses a new 64-bit Fortran compiler, fixes a number of bugs and eliminates a few mysterious crashes. Please report problems. The version number now refers to a specific snapshot of the source code enabling us to better identify and fix bugs.

Key changes between v14.6237 and 14.6720
64-bit compiler, bundle mkl math libraries – improved stability. Updated icon.
Improved SHELX import for atoms on special positions, SADI, DFIX and MPLA restraints, long form factors.
Spot is_nan in plot data.
New set of displacement parameter restraints, including TLS.
Better #CHECK output for restraints – including individual leverages.
Fix misreport of symmetry operators in CIF for C2/m
Dynamic threshold of Q peak height in Fourier peak viewer script.
Allow paths containing single quotes.
Add greek symbols to text and graphs for more concise display.
Leverages calculation via #sfls, refine punch=leverages, end
Changes related to getting consistent results for Thmax in CIF
Fixed listbox operation clicking in list now generates appropriate feedback for scripts.
Least squares matrix condition number output now included for problem refinement diagnosis.
Avoid almost infinite loop looking for bonds if atom coords have gone bad. Side effect – bonds outside +/- 50 unit cells of the origin won’t be found.
New choice of matrix invertors for SFLS. Default can be set in L23.
Fix default hkl format when re-reading ‘from-cif.hkl’ files (3F4.0,2F10.0).
Add a few more instrument/diffractometer types (synchrotron, neutron sources, etc.)
Modify platanom calculation: (i) use more d.p for improved precision; (ii) use c and d terms to correct data with all anomalous scattering effect removed as detailed in final version of ‘HUG and SQUEEZE’ manuscript.
Compute dispersion correction terms and photon interaction cross section for non-standard (=Mo,Cu) wavelength data. Alter xinlist3 to streamline experience.
Undo dialog: fix situation where current L5 is marked as error list.
Check for isotropic / unknown atoms before attempting to SPLIT in xsplits.ssc
Make L11 depend on L28, now if L28 filters change the VCV becomes invalid, require re-refinement. Avoids publishing CIF after omitting reflections without extra cycles.
Fix storage of converge checkbox state so it isn’t overridden when called from xwrite5.
Edlist3: revamp user interface to simplify. Added get/set mu values from L29 for each element.
Add Helium to properties file.
LIST 6 version incremented to 124. NEW DSC files will not be backwards compatible with older versions of CRYSTALS.
Better treatment of twins in Fourier maps.
Fix output of RIDE constraints (better refinement stability).
Reduce decimal places for angles with no esd (e.g. by symmetry constraint, or not refined) from 3 to 2 in CIF output. Avoids reporting e.g. 179.995 degress for exactly 180 degree angles.
Add internal vs external variance plot
Fix switch on of extinction from the Guide ‘Add extinction parameter’ dialog.

 

Oct 232017
 

Acta Crystallographica, 2017, C73, 845–853. [ doi:10.1107/S2053229617013304 ]

Using an approximate correction to the X-ray scattering from disordered, resonantly scattering regions of crystal structures we have developed and tested a procedure (HUG) to recover the absolute structure using conventional Flack x refi nement or other post-re finement determination methods.

Oct 102017
 

Lewis is working on a project to improve our understanding of modulation in molecular materials by studying analogues of Barluenga’s Reagent.

Away from the lab Lewis enjoys sports including football, rugby, and American football, as well as the odd game of FIFA.

He was inspired to join the group after attending the Structural Methods Options Course. His favourite space group is I-43d and he is equally happy programming in Fortran or Python.

Oct 082017
 

Gwenno is investigating methods for determination of flexible organic molecular structures using the atomic pair distribution function.

Around labs, Gwenno manages to fit in singing, acting, dancing and painting, and enjoys skiing.

 She still prefers programming in Python 2 over Python 3, and her favourite XC functional is LDA (who knew?).
Oct 082017
 

Oli Bar is investigating geometric parameters of metal organic frameworks using data analysis tools and machine learning.

To unwind after a hard day of Python algorithms he plays tennis and badminton, and enjoys swimming. He prefers the non-standard setting of space group 14, P21/n, and at the time of writing he is undecided on his favourite exchange correlation functional.

Oct 082017
 

Kiaora’s research project is to determine the structures of molecules which are liquids at room temperature or otherwise hard-to-crystallize using crystalline host frameworks and/or low temperature in-situ crystallization techniques.

While away from the lab Kiaora indulges in the incompatible sports of baking and swimming.

Her favourite space group is P21/c and she prefers the hydrogen bond over other types of intermolecular interaction.