Richard Cooper

Mar 272017

The CRYSTALS v14.6236 installer is now available.

This update fixes a number of bugs and eliminates a few mysterious crashes. Please report problems. The minor component or the version number now refers to a specific snapshot of the source code enabling us to better identify and fix bugs.

Key changes between v14.5841 and 14.6236
Ensure copied text is flushed to clipboard on CRYSTALS exit (otherwise it gets lost).
Upgrade xinvert script to accommodate the 11 enantiomorphic space groups and the 7 which require origin shifts.
Diffin: Set default for Z in case no formula found.
Diffin: Extend filename length to 512 to help when running in folders with long paths
Catch crash on matrix inversion of singular matrices.
Xcif: Disable ‘Include HKLI’ and ‘Include squeeze’ if include files not present in folder.
Xafour: Change limiting density question to a dialog to avoid new user confusion.
Close xpublish window after CIF dialog is dismissed.
Add CHANGE RESIDUE to pop-up menus
Speed up plots of internal vs external sigmas
Fix style and centre of rotation of zoomed objects. Add more ‘zoom’ and ‘unzoom’ options to menus
Improve popup text on model toolbar buttons
Add SWAP directive to #EDIT. This swaps the atomic and thermal parameters of pairs of atoms.
Insert residues numbers of generated hydrogen atoms
Sanity check of parameter values when loading from disk. Replace NaN with 0.0 or 1.0 as appropriate.
Show scale factor for electron densities, fix NANs in(Fo^20Fc^2) pattersons.
Cameron: Keep outline of small atoms at smaller scales.
Added header to design matrix ASCII output
Tabbed plot of Internal vs External variances
Insert appropriate occupancy and part # for H’s adjacent to split groups.
Spot clashing H-serial numbers on the fly and correct.
Increase allocation for lexical list processing (was falling over at 500 CONTINUATION lines, should now stretch to 2000).
Extend scattering factor look-up table out to Rho = 3.0
Enable unusual anomalous scattering factors to be input directly from the Cell/SG tab.
Add code to List 12 processing to catch singularities in rigid body code. Least useful rotational parameters are removed from the least-squares.
Enable LIST 2 to be output in full (#PUNCH 2) or just as the symbol (#PUNCH 2 B). This latter enables CRYSTALS to create an appropriate LIST 14 on re-input, otherwise the user must create it.
Changed handling of reflection sigmas. #LIST 6 now has an extra item, L30UP, which controls whether LIST 30 is updated as reflections are read in.
xregulh left SCPQ open, which meant that xwrite5 failed to delete it, resulting in the H optimisation list of refinable atoms being left in there and used to setup L12 if, and only if, there were no OH or NH atoms to be refined. FIXED.
Context menu entry to swap two atom labels.
Read SHELX T .res files (ignore peak height – last column in atom-coordinate list)
Added EXPORT button to FO vs FC graph (csv format).
Extended support for 6-digit H atom serial numbers to xwrite5.scp (not supported everywhere, but here is quite critical).
Improve treatment of A&B parts. Phase shift is included in A&B as they are stored for compatibility with PLATON SQUEEZE, then removed as they are used and the Phase shift applied separately.
Provide clear warning when link for PLATON fails because of a missing LIST
Fix reported cell volume e.s.d for tetragonal and cubic systems (includes correlation of length parameters).
NEW #PUNCH 6 I punches all stored keys.
Use bond list for auto H addition. Use part numbers to generate multiple H conformations on nearby atoms.
Manual ADD H (right-click Add hydrogens) now puts the new H’s into a sensible PART based on connected atom parts. Quite useful.
Allow automatic ‘ride’ of multiple part H’s on same carbon atom (previous version repeated the pivot atom in the constraints list).
Keeping CheckCIF happy: Suppress ESD output on H-bond angle (D-H–A) if the H is riding or fixed.
Add KEYS to reflection statistic plots. Add +/- 10% bands to npp.

Mar 112017

George is developing machine learning methods for classification and visualisation of experimental data. The first part of his project involves identification of metabolite changes in plants under changing environmental conditions, including the effect of auxinic herbicides. He is also looking at formulation of these herbicides to find ways of increasing their efficiency and reducing environmental impact.

In his spare time George may be found running.

Mar 112017

Laura is testing properties of new formulations of pharmaceutical materials. She is aiming to measure and understand the changes in dissolution rate of common pharmaceuticals when they are cocrystallised with different coformers.

In her spare time Laura swims, runs and cycles as part of the University Triathlon Team.

Mar 112017

James is investigating partial proton transfer in a hydrogen bond in some multi-component molecular materials. He is using single crystal diffraction, solid state NMR and computational modeling.

James tempers his enthusiasm for solid state chemistry by playing mixed lacrosse for the University.

Nov 242016

J. Chem. Inf. Model., 2016, 56 (12), 2347–2352 doi: 10.1021/acs.jcim.6b00565

A new molecular descriptor, nConf20, based on chemical connectivity, is presented which captures the accessible conformational space of a molecule. Currently the best available 2-dimensional descriptors for quantifying the flexibility of a particular molecule are the rotatable bond count (RBC) and the Kier flexibility index. We present a descriptor which captures this information by sampling the conformational space of a molecule using the RDKit conformer generator. Flexibility has previously been identified as a key feature in determining whether a molecule is likely to crystallize or not. For this application, nConf20 significantly outperforms previously reported single-variable classifiers and also assists rule-based analysis of black-box machine learning classification algorithms.

Publisher’s Copy

Sep 192016

Acta. Cryst. (2016) B72 661-683 (Feature Article) [ doi:10.1107/S2052520616012890 ]

surfaceDirect determination of the Flack parameter as part of the structure refinement procedure usually gives different, though similar, values to post-refinement methods. The source of this discrepancy has been probed by analysing a range of data sets taken from the recent literature. Most significantly, it was observed that the directly refined Flack (x) parameter and its standard uncertainty are usually not much influenced by changes in the refinement weighting schemes, but if they are then there are probably problems with the data or model. Post-refinement analyses give Flack parameters strongly influenced by the choice of weights. Weights derived from those used in the main least squares lead to post-refinement estimates of the Flack parameters and their standard uncertainties very similar to those obtained by direct refinement. Weights derived from the variances of the observed structure amplitudes are more appropriate and often yield post-refinement Flack parameters similar to those from direct refinement, but always with lower standard uncertainties. Substantial disagreement between direct and post-refinement determinations are strongly indicative of problems with the data, which may be difficult to identify. Examples drawn from 28 structure determinations are provided showing a range of different underlying problems. It seems likely that post-refinement methods taking into account the slope of the normal probability plot are currently the most robust estimators of absolute structure and should be reported along with the directly refined values.

Publisher’s copy

Aug 022016

Acta. Cryst. (2016) B72(4), 439-459 [ doi:10.1107/S2052520616007447 ] A. M. Reilly, R. I. Cooper, C. S. Adjiman, S. Bhattacharya, A. D. Boese, J. G. Brandenburg, P. J. Bygrave, R. Bylsma, J. E. Campbell, R. Car, D. H. Case, R. Chadha, J. C. Cole, K. Cosburn, H. M. Cuppen, F. Curtis, G. M. Day, R. A. DiStasio Jr, A. Dzyabchenko, B. P. van Eijck, D. M. Elking, J. A. van den Ende, J. C. Facelli, M. B. Ferraro, L. Fusti-Molnar, C.-A. Gatsiou, T. S. Gee, R. de Gelder, L. M. Ghiringhelli, H. Goto, S. Grimme, R. Guo, D. W. M. Hofmann, J. Hoja, R. K. Hylton, L. Iuzzolino, W. Jankiewicz, D. T. de Jong, J. Kendrick, N. J. J. de Klerk, H.-Y. Ko, L. N. Kuleshova, X. Li, S. Lohani, F. J. J. Leusen, A. M. Lund, J. Lv, Y. Ma, N. Marom, A. E. Masunov, P. McCabe, D. P. McMahon, H. Meekes, M. P. Metz, A. J. Misquitta, S. Mohamed, B. Monserrat, R. J. Needs, M. A. Neumann, J. Nyman, S. Obata, H. Oberhofer, A. R. Oganov, A. M. Orendt, G. I. Pagola, C. C. Pantelides, C. J. Pickard, R. Podeszwa, L. S. Price, S. L. Price, A. Pulido, M. G. Read, K. Reuter, E. Schneider, C. Schober, G. P. Shields, P. Singh, I. J. Sugden, K. Szalewicz, C. R. Taylor, A. Tkatchenko, M. E. Tuckerman, F. Vacarro, M. Vasileiadis, A. Vazquez-Mayagoitia, L. Vogt, Y. Wang, R. E. Watson, G. A. de Wijs, J. Yang, Q. Zhu and C. R. Groom

predictionsThe sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field.

Publisher’s copy

Jun 232016

mercerAlex is undertaking a research project attempting to automatically model severe disorder with crystal structures using a Monte-Carlo approach. Alex is firmly in the computational side of the research group avoiding any crystallisation or actual diffraction at all costs.