Richard Cooper

Sep 262020
 

Chemistry 2020, 2(4), 796-804; DOI: 10.3390/chemistry2040052

The Flack Parameter is now almost universally reported for all chiral materials characterized by X-ray crystallography. Its elegant simplicity was an inspired development by Howard Flack, and although the original algorithm for its computation has been strengthened by other workers, it remains an essential outcome for any crystallographic structure determination. As with any one-parameter metric, it needs to be interpreted in the context of its standard uncertainty.

Jun 232020
 
Clockwise from top left: Natalie Haarer, Aditya Desai, Noah Francis, George Sackman, Richard Cooper, Andre Frade.

This year’s Part II students have risen to the challenge of working remotely for three months, and celebrated handing in their research theses this week. Watch this space for publications arising from their investigations.

May 202020
 

The CRYSTALS 15.0.1 (v7809) installer for Windows 7/10 is now available. This is a quick patch release following the release of v7795.

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

Key changes between 15.7795 and 15.7809

This is a small patch release which fixes a couple of broken URLs, adds some new icons, new shortcut keys, quick access to import and export via toolbar.

Key changes between 14.6999 and 15.7795

This release of CRYSTALS has changed the way the software is installed, so that you don’t need administrator permission to install or run it.
If you have an old version of CRYSTALS installed, and you follow the prompt to uninstall it, it will require administrator permissions. If you do not uninstall the old version there may be duplicated information in different parts of the registry, but it should not prevent use of the software.

The new install structure brings CRYSTALS closer to best practice for installing applications on Windows, and as a result you can no longer find the application and examples in c:\wincrys\

While this will be distressing for users from the days of the command line, it shouldn’t affect point-and-click users very much. Application and supporting files can be found in

%LOCALAPPDATA%\Programs\crystals

and demo files are in

%APPDATA%\crystals\demo

If you need to access demo files or edit CRYSTALS scripts, you can paste the locations above into a Windows Explorer, or find shortcuts to both of these locations in the Windows start menu in the Crystals group.

Other changes since v14.6999 (July 2018):

  •  Added ‘cycle residue’ button to toolbar. Eases working with large structures. See: https://www.youtube.com/watch?v=sN7w-THNmTo
  • Added ‘cycle parts’ button to help visualise disorder parts: https://youtu.be/OoRm9J7hfjE?t=268
  • Added ‘restrain templates’ to list 16 editor. Work in progress, see demo here: https://www.youtube.com/watch?v=R3SHqKv9pCg
  • Improved refinement mode override for individual atoms. Video here: https://www.youtube.com/watch?v=sCTV4HN8RDk
  • Catch instabilities during matrix inversion, allow user to choose precision or speed in GUI
  • Improved undo structure dialog. Catch cases with lists marked as ‘in error’. Structure is shown automatically when selecting.
  • Reflections with a weight of zero are excluded from the total count.
  • Output files (listing, punch, mon) and many intermediate data files are now stored in subfolders of your working directory to keep it tidier.
  • Additional colours added to colour tables for atom types.
  • Removed dependency on CRYSDIR environment variable when launched from command line. Will override if set, but otherwise .exe location is used.
  • Sort deuterium with H in CIF formula.
  • Peak height slider added to find H dialog, use it to hide low density peaks. Improved usage with neutron H maps.
  • Slant Fourier dialog now computes default size limits which encapsulate the selected atoms.
  • Fix cell su issue when importing data from .ins files (and other bugfixes for edge cases in shelx2cry)
  • Fix sorting of data in Mogul dialog window (regression)
  • Fix reading of squeeze data from PLATON (regression)
  • Fix Cameron (regression)
  • Changed behaviour: if you click a link to a file in the working folder in CRYSTALS text window (e.g. publish.cif) it opens in Windows Explorer instead of the default application.
  • Upgraded MCE.
  • Text output simplified, especially SFLS.
  • Added Find and Replace dialogs to internal text file editor (e.g. for editing L12 and L16).
  • Updated icons.
  • Get WinGX location from the registry rather than environment variable.
  • Historically Fourier map units are scaled by 10.0 to give 10 x e-/A^3 (e.g. in MCE or MapView). Command line default remains same for compatibility, but the GUI difference Fourier dialog now uses a scale factor of 1.0
  • Added logging of file closures in .log file – easier to track which script or input file commands were from.
  • Shelx2cry will now automatically import hkl if given a path to a different folder.
  • Some renaming of CIF data items for filtered sets of data for compatibility with CheckCIF. All output is still present, comments in CIF explain the reasoning.
  • Added electron radiation type. Scattering factors (eight-term approximation) for electrons included L.-M. Peng (1999) Micron 30, 625-648.
  • Remember preference (per-structure) for refining occupancy of PARTS when using the Guide (saves unchecking box for every refinement setup).
  • Default CRYSTALS merge updated to ignore large outliers. Will effect some noisy datasets if they are re-imported. 
  • Fixed Invert structure option in Structure menu.
  • Fixed ‘change to uequiv’ popup menu 
  • Fixed ‘set Uiso’ popup menu item 
  • Many small bug fixes and improvements. Full commit history and changes at https://github.com/ChemCryst/crystals/
May 142020
 

The CRYSTALS 15 (v7795) installer for Windows 7/10 is now available.

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

Key changes between 14.6999 and 15.7795

This release of CRYSTALS has changed the way the software is installed, so that you don’t need administrator permission to install or run it.
If you have an old version of CRYSTALS installed, and you follow the prompt to uninstall it, it will require administrator permissions. If you do not uninstall the old version there may be duplicated information in different parts of the registry, but it should not prevent use of the software.

The new install structure brings CRYSTALS closer to best practice for installing applications on Windows, and as a result you can no longer find the application and examples in c:\wincrys\

While this will be distressing for users from the days of the command line, it shouldn’t affect point-and-click users very much. Application and supporting files can be found in

%LOCALAPPDATA%\Programs\crystals

and demo files are in

%APPDATA%\crystals\demo

If you need to access demo files or edit CRYSTALS scripts, you can paste the locations above into a Windows Explorer, or find shortcuts to both of these locations in the Windows start menu in the Crystals group.

Other changes since v14.6999 (July 2018):

  •  Added ‘cycle residue’ button to toolbar. Eases working with large structures. See: https://www.youtube.com/watch?v=sN7w-THNmTo
  • Added ‘cycle parts’ button to help visualise disorder parts: https://youtu.be/OoRm9J7hfjE?t=268
  • Added ‘restrain templates’ to list 16 editor. Work in progress, see demo here: https://www.youtube.com/watch?v=R3SHqKv9pCg
  • Improved refinement mode override for individual atoms. Video here: https://www.youtube.com/watch?v=sCTV4HN8RDk
  • Catch instabilities during matrix inversion, allow user to choose precision or speed in GUI
  • Improved undo structure dialog. Catch cases with lists marked as ‘in error’. Structure is shown automatically when selecting.
  • Reflections with a weight of zero are excluded from the total count.
  • Output files (listing, punch, mon) and many intermediate data files are now stored in subfolders of your working directory to keep it tidier.
  • Additional colours added to colour tables for atom types.
  • Removed dependency on CRYSDIR environment variable when launched from command line. Will override if set, but otherwise .exe location is used.
  • Sort deuterium with H in CIF formula.
  • Peak height slider added to find H dialog, use it to hide low density peaks. Improved usage with neutron H maps.
  • Slant Fourier dialog now computes default size limits which encapsulate the selected atoms.
  • Fix cell su issue when importing data from .ins files (and other bugfixes for edge cases in shelx2cry)
  • Fix sorting of data in Mogul dialog window (regression)
  • Fix reading of squeeze data from PLATON (regression)
  • Fix Cameron (regression)
  • Changed behaviour: if you click a link to a file in the working folder in CRYSTALS text window (e.g. publish.cif) it opens in Windows Explorer instead of the default application.
  • Upgraded MCE.
  • Text output simplified, especially SFLS.
  • Added Find and Replace dialogs to internal text file editor (e.g. for editing L12 and L16).
  • Updated icons.
  • Get WinGX location from the registry rather than environment variable.
  • Historically Fourier map units are scaled by 10.0 to give 10 x e-/A^3 (e.g. in MCE or MapView). Command line default remains same for compatibility, but the GUI difference Fourier dialog now uses a scale factor of 1.0
  • Added logging of file closures in .log file – easier to track which script or input file commands were from.
  • Shelx2cry will now automatically import hkl if given a path to a different folder.
  • Some renaming of CIF data items for filtered sets of data for compatibility with CheckCIF. All output is still present, comments in CIF explain the reasoning.
  • Added electron radiation type. Scattering factors (eight-term approximation) for electrons included L.-M. Peng (1999) Micron 30, 625-648.
  • Remember preference (per-structure) for refining occupancy of PARTS when using the Guide (saves unchecking box for every refinement setup).
  • Default CRYSTALS merge updated to ignore large outliers. Will effect some noisy datasets if they are re-imported. 
  • Fixed Invert structure option in Structure menu.
  • Fixed ‘change to uequiv’ popup menu 
  • Fixed ‘set Uiso’ popup menu item 
  • Many small bug fixes and improvements. Full commit history and changes at https://github.com/ChemCryst/crystals/
Mar 122020
 

CrystEngComm, 2020, DOI: 10.1039/D0CE00111B

The performance of a model is dependent on the quality and information content of the data used to build it. By applying machine learning approaches to a standard chemical dataset, we developed a 4-class classification algorithm that is able to predict the hydrogen bond network dimensionality that a molecule would adopt in its crystal form with an accuracy of 59% (in comparison to a 25% random threshold), exclusively from two and lower dimensional molecular descriptors. Although better than random, the performance level achieved by the model did not meet the standards for its reliable application. The practical value of our model was improved by wrapping the model around a confidence tool that increases model robustness, quantifies prediction trust, and allows one to operate a classifier virtually up to any accuracy level. Using this tool, the performance of the model could be improved up to 73% or 89% with the compromise that only 34% and 8% of the total set of test examples could be predicted. We anticipate that the ability to adjust the performance of reliable 2D based models to the requirements of its different applications may increase their practical value, making them suitable to tasks that range from initial virtual library filtering to profile specific compound identification.

Oct 172019
 

Nature 574, 390–393 (2019). [ doi: 10.1038/s41586-019-1616-2 ]

We report the isolation and structural characterization of a simple coordination complex in which six ligands form bonds with a central transition metal in a hexagonal planar arrangement. The structure contains a central palladium atom surrounded by three hydride and three magnesium-based ligands. This finding has the potential to introduce additional design principles for transition-metal complexes, with implications for several scientific fields.

  • Publisher’s copy: Nature 574, 390–393 (2019)
Oct 042019
 

Noah is researching development of better descriptors of molecules for use in machine learning to prediction of crystal properties. Despite being stuck in the basement, Noah’s favourite building on the Chemistry estate is the CRL. His favourite functional is B3LYP and when not in the lab he plays hockey and 5-a-side football.

Oct 042019
 

Aditya is developing machine learning methods for predicting the classification of various crystallographic properties. He mostly works with Python 3 and associated ML and DL libraries.

In his spare time he enjoys baking and hiking. His go to space group is Fmmm and his favourite intermolecular interaction is pi-pi stacking – classic.

Oct 042019
 

Natalie is implementing a scattering model for chemical groups which behave as “hindered rotors” to the base Fortran code of the CRYSTALS software. The representation requires fewer parameters and is more physically realistic than current models. Look out for better trifluoromethyl groups in future!

Natalie does not have a favourite programming language, believing instead that we should use the appropriate tool for the problem being solved. In her spare time she is a keen cross-country runner and has completed over 170 parkruns.