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/
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.

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