Enhanced Precision for Hexagonal & Trigonal Crystals. SingleCrystal now provides the option (on by default) of automatically detecting "hexagonal" fractions (1/6, 1/3, 2/3, 5/6) in input data, and converting these to full 64-bit precision. Conversion happens in two places: when importing data from a text file (e.g., a CIF) or when using the Crystal Editor. This option can be disabled via a new checkbox in the Simulation pane of the Preferences panel.
Miscellaneous. This version includes a new library file plus minor bug fixes.
Added the crystal structure of CoNb3S6 to the integrated structures library.
The Mini Stereogram again shows axial poles for new structures.
Improved Auto Grid Algorithm. Addressed an issue that prevented some patterns from having their periodicities identified. We now average over multiple grid options, resulting in a more reliable view calculation. (This is a major improvement on the former Auto Grid command.)
Improved Stereogram. The Stereogram now includes a new option to only show South-hemisphere projections, and these poles now have a smarter appearance; the mini stereogram also adapts to these settings.
Added option to show only South projections (thereby hiding any North projections). Some scientists (including Geologists) like to see just the South hemisphere. This has required a change to the Projections group of the Stereogram Inspector.
The Mini Stereogram now adapts to the North/South hemisphere settings. If both North and South hemisphere projections are specified, we continue to show just the North ones; however, if only South projections are specified these will be shown in the mini stereogram (without any North projections).
South-hemisphere poles now use thicker rims as their radii increase. We also now fill these with the background.
Tabulated Observed Intensities. The Reflexions List now automatically displays any observed peaks: their positions and intensities (using whatever default settings have been specified for peak markers).
Output Log. Added an "Output Log" command to the View menu. This displays a new text output window. It includes more detailed information about program operations, including grid fitting.
Improved Gallery Window. The Gallery window sports a new look, with icons for each group. In addition, four new video tutorials have been added, covering "Auto Grid", "Diffraction in 3D", "Brillouin Zones" and "Fourier Transforms".
Miscellaneous Changes. This version includes a large number of miscellaneous enhancements and occasional bug fixes.
Improved the Grid Inspector: the obliquity reset button now has a standard "Go Back" icon, instead of the confusing "90°" title. The "bearing" group now has a stepper control and a reset button (which resets the Grid to the nearest perpendicular).
Export Graphics format, magnification and transparency are now saved as preferences preferences and restored next time the program is launched.
Slightly faster algorithm for calculating the approximate view direction.
Arbitrary stereogram poles can now be added, even if their indices are way outside our ±999 range. If we detect an out-of-range pole, we add the closest in-range pole. For example, (1230 230 1) would get (476 89 0) and an advisory message would be shown.
The User's Guide, "What's New" and Tutorial documents have all been updated for this release.
Changed behaviour for Poles Inspector. Double-clicking the indices of a group row now edits the group (rather than expanding or collapsing it, as before).
Added ability to tab from one Poles Inspector position field to the next.
Fixed an issue with merging sites that have the same fractional coordinates but different site occupants. Normally this would work, but if the resulting occupancy sum exceeded 1.0 (which might happen because of limited numeric precision) then the merge would fail.
Fixed a bug with the crystal Info display. The number of formula units per cell (Z) was incorrect for monatomic structures.
Fixed an issue with the view direction pop-up: applying a preset orientation two o more consecutive times was not working correctly not even when the view direction had changed.
Fixed an issue in the Poles Inspector: new pole command (actions menu) was actually editing pole not adding a new one when a pole was selected in the list.
Single-clicking in the 3D diffraction pane now correctly stops the spinning.
The Stereogram pane now correctly allows a choice of window background or diffraction background.
Diffraction and Stereogram relative sizes are now restored properly from session files.
Miscellaneous Changes. This release fixes an occasional bug with Grid-based auto indexing and a cross-platform formatting problem relating to custom background subtraction.
Fixed a rare issue in which Grid-based auto-indexing could fail for certain structures.
Addressed a problem with saving custom background subtraction data in the document file. The Mac and Windows versions were using a different format, which prevented these data from being shared between platforms.
Improved Export Graphics experience. The Export graphics command now saves the settings (format, magnification and use transparency) as user preferences, so you don't have to reset the default values every time!
Miscellaneous Changes. This release fixes issues relating to site occupancies, high-DPI screens and pixel formats.
Fixed an issue merging sites with the same fractional coordinates but different occupants. The problem happened if the resulting occupancy added up to 1 and due to numeric precision the merge could fail.
Fixed different bugs manipulating picture patterns in high DPI screens, the DPI value was not being taken into account when making the calculations (e.g. grid fitting or auto indexing).
Fixed a bug loading images with 1 byte per pixel format, resulting in a blank image.
Fixed a very-specific issue for annual licences expiring in the month of December, which could cause a crash when attempting to display the "About" window.
Improved Interface. The document window gets some general interface tweaks designed to improve the overall user experience.
The Reflexions List now uses a dynamic icon for the horizontal/vertical toggle control: this changes according to the layout mode. This icon and its neighbouring "Close" icon are now always visible.
Miscellaneous Changes. This version includes minor updates and compatibility improvements for software licensing
Toolstrip. The popover controls for screen tools and overlays have been replaced by a new Toolstrip, located beneath the main Toolbar. This provides easier, one-click access, and can be hidden if required by clicking the new Tools toolbar button (or by choosing: View > Screen Tools > Hide Tools).
The former View popover has been replaced by separate buttons for each View; of these, the Reflexions button is included in the default toolbar configuration.
Support for High Dynamic Range images. SingleCrystal can now import and display high-dynamic-range (HDR) image files, such as those from the new generation of solid-state detectors.
Not only can HDR data be read into the program, but their intensity variation is made visible thanks to an automatic gamma conversion which remaps the intensity scale to work with the 8-bit display (256-levels) of most monitors. Note that the original, raw intensities, are displayed via peak markers and can be exported.
Real-Time Readout for Observed Images. When using the Arrow tool, the mouse position and corresponding observed intensity are displayed via an "Info Tip" at the bottom of the Diffraction Pane. Note that HDR images also show the original, raw intensity.
Radially-Averaged Background. A new "Radial average background" option has been added to the Background Detection popover in the Picture Inspector. With this option in effect, the background bytes are averaged, radially, about the screen centre.
Important: you may need to physically move your obsered pattern (e.g., using the Move tool) to ensure that its centre of intensity is centred in the Diffraction Pane. (Displaying the Crosshairs will make this easier!).
Generate Ring Pattern. This new option on the Pattern menu will convert an existing picture pattern to a series of concentric rings - useful for comparison with powder diffraction data. (Note: as with the radially-averaged background option, you should ensure that your observed diffraction image is correctly centred before using this command).
New Window Appearance. The document window has been redesigned to match the general look of CrystalMaker 11. The integrated toolbar has been removed and in its place are separate titlebar and toolbars (the latter with a lighter background theme). New icons have been added as well as segmented button designs.
Miscellaneous Changes. This version includes a large number of miscellaneous enhancements and occasional bug fixes.
Improved inspector behaviour: when using our (default) disclosure group "auto closure" mode you can hold down the shift key to open multiple disclosure groups.
Renamed the Picture Inspector's Background group as "General", to avoid confusion with the background subtraction process.
The Registration and Support links in the Gallery window automatically populate more fields in the corresponding web forms.
Updated "What's New" guide.
The screen tool is now correctly shown at startup.
Changing the screen tool in one window now causes it to change in all other windows.
Updated crystal structures libraries. New crystal structures have been added for Nontronite (a smectite mineral) and Montmorillonite (replacing a calculated structure with a real one).
Added new icons for the Sidebar, Inspector, Log and Gallery.
Fixed memory leaks with the Gallery- and Document windows.
Darker Gallery background.
Fixed a crash initializing the 3D render system.
Fixed an issue displaying markers on high DPI screens.
The magnify tool now centers the pattern in the correct clicked point.
The Levels histogram now updates correctly when changing the minimum and maximum threshold values.
Redesigned Reflexions header (as for the Mac version).
SingleCrystal 5 now runs again correctly on Windows 7.
Streamlined Document Interface. SingleCrystal 5 has a sleek, modern interface design with smart inspectors and animated controls. Inspectors will switch between 2D, 3D, Crystal Shape and Stereogram versions as your visualize content changes, and/or you click in different panes.
Document Notes. You may notice that all of the examples in SingleCrystal's Gallery window show notes on the right-hand side. These notes are designed to be informative, and you can use this region to record notes about your own diffraction experiment using rich text formatting.
Notes are document-wide (independent of pattern selection). You can switch between displaying Notes or the Parameters Inspector, using the Notes and Parameters segments of the Inspector segmented control.
Floating "Mini Stereogram". As an aid to orientation, SingleCrystal 5 includes the option of a floating "Mini Stereogram", which appears over the Diffraction Pane, "docked" to an edge or corner. (This replaces the stereogram shown in SingleCrystal 4's Inspector.)
The Mini Stereogram is designed to be visually unobtrusive (and may be hidden if desired) but it also includes useful shortcuts for showing the full (and editable) Stereogram Pane and the Poles List.
Diffraction in 3D. SingleCrystal 5 uses the latest 3D graphics from Apple ("METAL") and Microsoft ("DirectX") to let you explore diffraction in 3D. Specifically, you can show the weighted reciprocal lattice as a 3D model, using the Simulate > 3D Weighted Reciprocal Lattice command. Here, each reciprocal lattice point is indicated by a sphere (or a symbol, for systematic absences) and you can add various planes, vectors - or even cones - corresponding to projections in your Stereogram.
Brillouin Zones. You can display the First Brillouin Zone for any material using the Simulate > 3D Brillouin Zone command. SingleCrystal shows the portion of reciprocal lattice around your Brillouin Zone, with points connected via lines parallel to the reciprocal lattice axes, x*, y* and z*.
You can customize the display of your Brillouin Zone (and optionally its surrounding reciprocal lattice) using the dedicated inspector.
You can click on face centres, edges and vertices to display their coordinates; shift-click to define a trajectory in reciprocal space.
Crystal Shapes An extension of SingleCrystal's 3D capabilities is the ability to display crystal morphologies. This is done in three stages:
Choose: Simulate > 3D Crystal Shape. If you haven't already defined any faces, then a default, unit cell shape, is shown.
Add any additional faces using the Faces inspector: click the + button (bottom- left-hand corner of the inspector) to show an editing dialog; notice that there is the option (recommended) to add symmetry-related faces.
Use the Distance sliders/text fields to specify how well-developed each face is. A larger distance (from the face to the centre of the crystal) results in smaller faces; reducing the distance makes faces larger. Note: this is sometimes referred to as a "Wulff Construction" - but there is nothing special about this.
Use the Shape inspector to specify a preset ("standard set") group of faces; set the colouring scheme, opacity and saturation of faces; move your shape away from the screen centre (useful when working with multiple shapes in the same document - e.g., for twinning or chiral relationships).
Fourier Transforms. SingleCrystal 5 lets you simulate an "optical diffraction" pattern for any simulated or observed pattern. You might, for example, wish to show a faux "high resolution TEM image" from an observed diffraction pattern; or you might wish to explore principles of diffraction by editing simple image "masks" and observed the simulated Fourier Transform.
You can either generate a static image, using the Pattern > Generate Fourier Transform command; or you can Show an interactive Fourier Transform (on the right-hand side of the Diffraction Pane), using the View > Diffraction > Show Fourier Transform command.
Note that you can combine multiple images from your Patterns List to change the resulting Fourier Transform. For example, you might wish to lock one pattern (perhaps a row of dots) and then move a second pattern (perhaps another row of dots) to see how changing the separation of the patterns changes the Fourier Transform.
SingleCrystal 5 includes a wide range of teaching resources for Fourier Transforms. These comprise a series of multi-pattern documents exploring principles of convolution and shape functions. You can locate the library inside the Gallery window.
Auto Grid. SingleCrystal can automatically detect the positions of intensity maxima in observed diffraction images. As part of this, when the Grid overlay is first shown above an observed image, the program will attempt to "snap" the Grid so that its nodes are superimposed above observed reflexions. (This is appropriate for techniques that image 2D reciprocal lattice sections, such as an X-ray precession pattern, or a TEM diffraction pattern.)
Once the Grid has been manually edited, it will no longer automatically "snap" into place (this is to protect your own measurements). However, you can manually "snap" the Grid into place using the Grid Inspector's Auto-Fit Grid button.
Auto-Index Patterns List & Phase ID. When using the Grid overlay to auto-index an observed diffraction image, one requires a simulated pattern, as reference. In earlier versions of the program this pattern would have been loaded into the program as the first, visible pattern.
SingleCrystal 5 now includes the option of using multiple simulated patterns as references for auto-indexing. This allows you to create your own shortlist of potential phases, and let the program choose which gives the closest match to the observed diffraction geometry.
Alternatively, you can specify:
One more sub-libraries from the integrated structures library;
All structures loaded from a specified folder (and any sub-folders). Structures should be in a suitable format (e.g., CIF, CMTX or CrystalMaker document, CMDX).
SingleCrystal will simulate the reciprocal lattice geometry for each structure (taking into account any systematic absences), and provide a shortlist of best-fit results in the Best-Fit popup-menu. You can visualize the results graphically, by choosing an item from the menu; SingleCrystal will load the corresponding structure, simulate its diffraction pattern, and display this in the best orientation over and above your observed diffraction image.
Peak Detection/Laue Auto Indexing. We have already mentioned SingleCrystal's ability to detect intensity maxima: this underpins the "Auto Grid" feature. Another aspect of this is the ability to auto-index diffraction patterns that don't show a reciprocal lattice geometry, e.g., Laue patterns. Note that, compared to Grid-based auto-indexing, this is considerably slower.
SingleCrystal can display intensity maxima using Peak Markers: circular objects of variable radius, overlaying the observed diffraction image.These can be used for measurements, allowing you to export a text file of peak positions and intensities - or even an indexed set of intensities, if you have successfully auto-indexed the pattern.
Import of DM3 & DM4 Files. SingleCrystal can now read from data files generated by the "Digital Microscopist" software from Gatan, in the "DM3" and "DM4" file formats.
Caveat: DM3 and DM4 are proprietary file formats, for which no (official) specifications have been published. We have had to deconstruct these formats, so cannot guarantee that file import will always be reliable. If you encounter problems, please send us your files so we can investigate.
SingleCrystal can load multi-structure files in these formats. However, it is not clear that any scaling information is accurate, so users will need to manually verify the correct picture scales (e.g., by calibrating with the Ruler overlay).
Levels Histogram & Gamma Control. SingleCrystal 4's Threshold control group has been replaced by a new Levels group, which also features an intensity histogram. You can visualize the spread of intensities and, if using gradient colouring, observed how the different colours reflect the differing levels.
An intensity slider, located below the histogram, includes Minimum and Maximum thumb controls, allowing you to optimize the colour range.
Another new feature is the ability to define an intensity "Gamma": letting you optimize the colouring by accentuating (or diminishing) extreme intensities. A Gamma slider is shown above the histogram. Notice that, by dragging this slider, the shape of the histogram changes.
Advanced Scattering Factors. Earlier versions of SingleCrystal relied on a single table of published X-ray scattering factors, as taken from the International Tables for Crystallography. The Mott Equation was then used to compute electron scattering factors. This worked well for most cases, but there were issues: the Mott Equation fails at very-low scattering angles; and the published data are not appropriate for high-angle scattering.
High-Angle Scattering Factors.
SingleCrystal 5 now uses the data of Fox et al 1989 to compute high-angle x-ray scattering factors for the range: 2 < (sin θ / λ) < 6 Å-1. These authors used a fourth-order polynomial to fit the angle-dependence of ln(fx) . Their coefficients are presented in Table 6.1.1.5 of the International Tables for Crystallography (Second Edition), Volume C.
During the course of this work, we discovered serious errors in the published high-angle data of Fox et al 1989, which had also made their way into the International Tables. The published results for Li, Mg, Si, Ni and Zr are completely wrong, with the authors' parametric fitted curves failing to pass through any of their raw data points.
Rather than rely on erroneous published data, we have generated our own fits for all elements between He (Z=2) and Cf (Z=98), and we use our numbers for high-angle calculations.
As a service to the wider crystallographic community, our findings - and corrected data - have been supplied to the International Union of Crystallography, for use in future editions of the International Tables.
Electron Scattering Factors.
In addition to using a second table for high-angle x-ray scattering factors, SingleCrystal 5 now uses a further two sets of data for low- and high-angle electron scattering factors (as taken from the International Tables for Crystallography).
As a result of these changes, we can be confident that SingleCrystal 5 provides more-reliable simulated intensities across a much wider range of scattering factors for both x-ray and electron diffraction.
Lossless Image Compression. Observed diffraction images are now stored in compressed format, inside SingleCrystal documents. The program uses a proprietary LZW-style algorithm to provide extremely fast, efficient and lossless image compression.
This is particularly noticeable for multi-pattern files, which can now be stored in a fraction of the size of older formats. For example, the Fourier Transform example files are all on the order of a few hundred kilobytes, compared to tens of megabytes previously.
Image Cleanup. SingleCrystal 5 includes a customizable "cleanup" command, featuring sophisticated background detection, removal and noise reduction. This is designed for older, film-based diffraction methods, making it easier to compare intensities without the effect of a large background intensity "bulge".
As part of the background subtraction, SingleCrystal samples the observed image at regular intervals, skipping regions identified as reflexions, and interpolating the remaining areas. The resulting image map can then be subtracted from the raw pixels, resulting in a cleaner display.
Other Changes. SingleCrystal 5 includes a plethora of "under-the-hood" changes, designed to improve usability and performance.
New-style application icon.
More-sophisticated Grid-based auto-indexing algorithm, with correction for out-of-zone reflexions appearing from closely-aligned zone axes (an issue with high-index zones for large unit cells).
New Rotator toolbar icon with angle display.
New View Direction toolbar button with drop-down menu for rapid selection of common directions.
Auto-Centring of observed patterns: using peak markers and the pattern symmetry to centre the pattern.
Ability to hide the origin spot or to define its relative intensity.
Ruler, Protractor & Grid are automatically zoomed & rotated with the main pattern.
Improved pattern rotation: rotating about screen centre, rather than individual pattern centres.
Keyboard shortcuts for screen tools: a = Arrow; v = Move; h = Hand; z = Magnify ("Zoom").
Minimum d-spacing can be specified for Laue simulations. A new Reset button updates the simulation to match the minimum wavelength. If the minimum d-spacing is too high (i.e., greater than half the minimum wavelength) then a warning triangle is shown.
Central rotation for Ruler. Hold down the shift key and drag one of the two ruler holes to cause it to rotate about its centre point.
Export observed pattern as a visible image, a raw image, or a background- subtracted image.
Redesigned Poles Inspector. At the bottom of the list is a new "+" drop-down menu button with commands to add all symmetry-related poles out to a maximum index. A Colour drop-down menu button includes commands for colouring by symmetry, by N, by Pole or by Pattern.
Faces Inspector. When working with crystal morphologies, any stereogram poles are shown in a dedicated "Faces" inspector, with distance distance sliders to allow adjustment of face sizes. 22 SingleCr ystal 5 What 's New?
Stereographic projections now use hollow circles or squares for south hemisphere projections. This is neater than trying to use a filled colour.
Added a new Observed preferences pane. This includes settings for peak markers, plus peak search and background search parameters.
Improved Scattering Factors preferences panel. This now has a segmented control, letting one switch between Electrons, X-Rays and Neutrons, with the scattering factor curve and data table duly updated.
Visible intensity now shown in reflexion peak tips. We indicate the visible intensity using the label "Ivis". This contrasts with the relative integrated intensity, "I/Imax ".
Export integrated intensities for plot markers, including the option of all indexed peaks. (Integrated intensity is calculated from the user-specified marker radius.)
Export Indexed Peaks. A new Export button in the Peak Markers group allows users to generate a text file with the integrated intensities of marked peaks and their corresponding Miller Indices.
Major improvement to the Resolution group of the Display Inspector. We now separate out the Pixel Density and Pixel Pitch options which were, previously, combined under the "Density" heading. To make more space, the slider controls for pixel density and pixel pitch are accessed via buttons, and displayed in their own popovers.
Improved gradients for picture patterns, using black as a starting colour ("Ice", "Heat" and "spectrum"). We have also added new Red, Blue and Green gradients.
Renamed the Display Inspector's Position group as Centre & Rotate. Moved the Auto Centre and Centre on Marker buttons from the Auto-Index group to here. Removed the Reset button as we have separate "Reset" buttons for the X and Y centring.
Tidied View menu with icons for our custom views/overlays. Note that we have moved the "Theme" option to the Pattern menu, where it is now part of the Colour Reflexions submenu ("Apply Theme"). We have also added a new Screen Tool submenu, which allows users to change the current document's screen tool, without the need for clicking in a window's toolbar.
Improved legibility for overlay tools. The Ruler, Protractor and Grid now take into account the colour of the observed picture, and update their highlight colours accordingly.
Translucent Ruler Profile window.
Grid-based auto-indexing now searches for, and rejects, cases where high- index zones result in reflexions from other zones appearing in the same pattern.
Added a new Rotate Left button to the Protractor Inspector.
Added keyboard shortcuts for Actual Pixels (cmd-1) and Scale to Fit (cmd-2).
New Zoom menu commands: Zoom In (cmd +) and Zoom Out (cmd –). For consistency, the Scale to Fit command has been renamed as: Zoom to Fit.
The Scale to Fit command now works for simulated patterns as well as for observed diffraction images.
Added a new command to the Ruler Profile contextual menu: Show Cursor at Centre. This is useful because the user can position the ruler centre over a peak and then visualize its profile, with the cursor indicating the peak centre.
Added a Format submenu to the Edit menu, to facilitate rich-text editing in the Notes Inspector (with associated command-key shortcuts).
Added a "magnify" button to the stereogram pane. Clicking this hides the Diffraction Pane and Reflexions List (if visible) and then a "zoom out" button is shown which reverses the effect
Smooth pane resizing behaviour, using "Core Animation".
The Gallery window now includes examples files for 3D Brillouin Zone, Reciprocal Lattice and Crystal Morphology.
Added an extensive library of Fourier Transforms to the Gallery, accessible via that window's Sidebar.
Extensive modification of source code, replacing Apple's "deprecated" calls with newer ones, and adopting new security protocols.
Detachable popovers for screen tools, overlays and views. When detached, the popovers are shown in a condensed mode, without text. The popovers are hidden when a window moves into the background, but return when the window is frontmost.
Detached popovers move with the document window. This makes it easier to work with floating "palettes" including the Rotator.