SingleCrystal Changelog

What's new in SingleCrystal 5.0.0.300

• 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.