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.

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.

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.

Apr 082016
 

group16The 2016 British Crystallographic Meeting Spring Meeting took place at the University of Nottingham from 4th – 7th April. Contributions from Chem. Cryst. staff and students were:

Jerome G. P. Wicker, Bill I. F. David & Richard I. Cooper
When will it Crystallise? (Talk in session: From Amorphous to Crystal)

Jo Baker & Richard I. Cooper
Making and Measuring Photoswitchable Materials (Talk in session: Young Crystallographers’ Satellite)

Pascal Parois, Karim J. Sutton & Richard I. Cooper
On the application of leverage analysis to parameter precision using area detector strategies (Poster)

Oliver Robshaw & Richard I. Cooper
The role of molecular similarity in crystal structure packing (Poster)

Katie McInally & Richard I. Cooper
Linking crystallization prediction, theory and experiment using solubility curve determination (Poster)

Richard I. Cooper, Pascal Parois & David J. Watkin
Non-routine single crystal structure analyses using CRYSTALS (Poster)

Alex Mercer & Richard I. Cooper
Fitting Disordered Crystal Structures by Simulated Annealing of an Ensemble Model (Poster)

 

Mar 072016
 

Acta. Cryst. (2016) C72, 261-267 [ doi:10.1107/S2053229616003570 ]

snipA study of post-refinement absolute structure determination using previously published data was carried out using the CRYSTALS software package. We show that absolute structure determination may be carried out optimally using the analyses available in CRYSTALS, and that it is not necessary to have the separate procedures absolute structure determination and no inter­est in absolute structure as proposed by Flack [Chimia (2014), 68, 26–30].

Publisher’s copy

Oct 082014
 

v14.5481The CRYSTALS v14.5481 installer is now available.

This update fixes usability problems related to new features in the latest series of releases. There may be a problem with OpenGL rendering on ATI graphics cards – please report problems if you see any ‘artefacts’ while viewing crystal structure models.

Version 14.60 onwards are built with a new compiler and libraries – therefore please report any unusual installation or usage problems.

Note the slight change in version numbering (v14.62 -> v14.5481) The minor component now refers to a specific snapshot of the source code enabling us to better identify and fix bugs in older releases.

Changes
See v1460 release for more changes.

Aug 172014
 

v1460The CRYSTALS v1461 installer is now available.

There are still some usability issues in this release. v1462 is expected soon (October 1st).

This is a bugfix release. It fixes the following problems in v1460: a crash on loading large datasets; line-ending issues with the new built-in editor; freeze in Cameron; display issues with atom labels in CRYSTALS.

Version 1460 and this release are built with a new compiler and libraries – therefore please report any installation or usage problems.

Changes
See v1460 release for changes.

May 152013
 

pascalPascal is a senior post-doctoral researcher working on refinement and analysis of diffraction from very short lived excited state chemical species. He obtained a PhD with Dr Mark Murrie at Glasgow University studying the effects of pressure on single molecular magnets, and has since held posts at Utrecht University and University of Nancy working on software development and time-resolved diffraction. Pascal maintains a personal blog on chemical and crystallographic software matters, and in his spare time enjoys hiking and genealogy.