What Was New?

1. SingleCrystal 5 Support. This version includes support for the forthcoming SingleCrystal 5, including live rotation and live diffraction modes.

2. Enhanced Structure Checking. When editing an existing crystal, or importing a new one, the program now performs additional checks to ensure that inter-axial angles are non zero and that their sums are less than 360°.

3. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • Update checking works with our new SSL-based web server.

   • Fixed an issue in which structures could appear to flash as they were relaxed.

   • Re-saving a library file now works correctly.

   • Changing the distance range in the Distance Explorer window no longer causes the program to hang.

1. Smarter Auto Rotation. You can now automatically rotate your structure about an optimum rotation axis, thanks to a revised Cell option in the Spin popover.

   The program chooses the best rotation axis, depending on the unit cell orientation. If a cell face normal is closest to the vertical, then that becomes the rotation axis (as in version 10.8). However, if one of the axial vectors is closest, it will be used, followed by one of the major lattice vectors, in the range –1 ≤ UVW ≤ +1.

   A further refinement is that the rotation should now appear rock solid, even when using large angular increments.

2. Prismatic File Import. This version can import structural data from a "Prismatic" data file. Such files—used for simulation of high-resolution TEM images—comprise a rectangular unit cell with basic site information.

3. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • Detached popovers are now closed when switching to another window. This prevents potential confusion when another document window comes to the front and popovers from the previous window appear above.

   • Fixed a very-rare bug involving the "Notes" field in CrystalMaker text (CMTX) files.

   • Fixed an issue with the crystal structure of Anhydrite, as including in the "Sedimentary Minerals" group of the library browser.

1. Powerful Auto Rotation. The "Spin" popover has been completely redesigned, allowing for structure- rather than screen-specific rotation, e.g., rotating about a specific bond or cell axis, and preserving the rotation axis as the structure is manually rotated.

   The new popover includes an option for “unlocked rotation”, whereby the rotation axis can be rotated (relative to the screen), such that the user can reposition a spinning cube, say. This makes it easy to record video with inclined rotation: great for showing a unit cell, or a spinning molecular group around an inclined rotation axis.

   Rotation axes can be defined parallel to the screen axes, the nearest unit cell axis—or entirely customized, via the angle fields. For the first time, oscillation mode can work about any axis: not just the screen Y axis.

   Structure Rotation Examples:

   • Rotation About a Cell Axis. Simply rotate your structure so that the desired unit cell axis is approximately vertical (i.e., parallel to the screen Y axis, which runs from bottom-to-top of the screen). Next, open the Spin popover (e.g., by clicking and holding down the mouse over the toolbar Spin button). Click the Cell preset, then click the Start Spinning button.

     Once your structure is spinning, you can manually rotate it (e.g., by clicking-and-dragging with the mouse) and still have the structure continue spinning about your chosen cell axis.

   • Rotating About a Lattice Vector. Firstly, choose the Transform > View Direction > Set View Direction command to orient your structure. Secondly, open the Spin popover and click the Z preset. Thirdly, uncheck the Lock Rotation Axis to Screen setting (important, as you want rotation relative to your structure). Finally, click the Start Spinning button.

     You should now be able to manually rotate your structure whilst it continue to spin about your original lattice vector.

   • Rotating About a Specific Bond. Select the bond, then choose the new Make Bond Vertical command (as described below). Next, open the spin popover, choose the "Y" rotation preset and ensure that the Lock Rotation Axis to Screen checkbox is unset.

     Once your structure is spinning, you can manually rotate it without affecting the auto-rotation axis (i.e., your selected bond axis).

   Note: you can record "rotation movies" about your structure-specific axes; just remember to specify the Custom (From Spin Popover) option when you choose the File > Export Video > Rotation Movie command.

2. New View Commands. New commands have been added to view the structure parallel to, or perpendicular to, an existing selection:-

   • Bond Selection. Users can now opt to view the structure along a selected bond, or to make that bond vertical. New View Along Bond and Make Bond Vertical buttons have been added to the Bond Selection Inspector.

   • Atom Selection. New View Along Atoms and Make Atoms Vertical buttons have been added to the Atom Selection Inspector.

   • General Selection. The Transform > View Direction submenu now includes a command to view perpendicular to the overall selection.

3. Nano Spirals. Redesigned the Bend Selection sheet to include a new Radial Offset field. This allows the one to define a spiral (instead of circular) section.

4. Mean distance from plane. The Calculate > Distance from Plane command now calculates the mean distance and standard deviation; these values are printed in the Output Log, after the individual distances.

5. Faster "Speed Sync". It is now possible to rapidly synchronize a multi-structure document by holding down the shift key whilst pressing the toolbar's Sync button. This skips saving a backup step (which can be a long-winded operating), allowing faster operation.

6. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • Replaced the former Transform > Spin menu command with a dedicated Spin submenu. This provides access to a dedicated keyboard shortcut (cmd-opt-I) as well as a new Adjust Spin command: an alternative way of accessing the Spin popover, for those unfamiliar with the technique of clicking-and-holding the Spin toolbar button.

   • Speedier popovers. Clicking a "delay" popover button (such as the Spin toolbar button) now causes the popover to appear after a shorter delay.

   • Exporting visible- or crystal-coordination output now results in unit cell parameters being added to the output file.

   • For the sake of clarity, removed the "duplicate" C222₁ space group settings corresponding to [bac], [bca] and [cba] settings. This leaves a single listing each for the axial settings, viz. C 222₁, B 222₁ and A 2₁22.

   • Improved molecular modelling results, with a new three-body potentials files containing revised values. A diagnostic output call - which could cause the program to bog down in certain cases - has been removed.

   • CIF files containing anisotropic temperature factors expressed in the (rarely used) B_ij format, are now imported correctly.

1. Extended CMTX (text) file format. CrystalMaker now saves the colours of individual sites in its CMTX format. Previously, only the dominant, "element" colour was saved; now, any sites whose colours differ from the dominant element colour, are included in the format's "TYPE" card.

   When composing a CMTX file manually, you can enter either an element symbol (e.g., "Si") or a site label (e.g., "T2i") in the TYPE definition, e.g.,

   TYPE
   Si 1.0 0.0 0.0 0.5
   T1 1.0 0.0 0.0 1.0
   T2 0.95 0.0 0.1 1.0
   O 1.2 1.0 0.0 0.0
   

   here, the element symbols "Si" and "O" have been included, together with two site labels, "T1" and "T2", which have "custom" colours.

   (We should emphasize that all site labels should be unique and different from any element symbols.)

2. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • When working in "Live Diffraction Mode", unit cell transformations (e.g., changing lattice type, supercell, surface cell) now trigger updates to the diffraction pattern.

   • Surface cells in extreme orientations (e.g., 331) can now be generated using larger, more-convenient, unit cells where the z-axis is perpendicular to (or nearly perpendicular to) the plane of interest.

   • Perfectly-flat molecules no longer appear hidden when depth fading is enabled.

   • Fixed a potential issue reading from CASTEP files via the File > Open with Format submenu. This option expected the file to be in CASTEP's "output" option, and failed to handle "density" or "cell" formats. Now, the program uses the file extension in order to differentiate the formats better.

   • Resolved an extremely-rare issue in which some bonds were drawn at incorrect angles, owing to numeric rounding errors.

   • Workaround for creating a supercell to cope with input atoms defined with fractional coordinates lying outside the unit cell (!). CrystalMaker now explicitly moves any offending sites into the correct unit cell before proceeding with its transformation.

   • Fixed an unlikely case where vast numbers of (dummy) element symbols might trip up the program's chemical formula calculation.

   • Workaround for a rare system timing issue which could cause the program to crash after attempting to merge a group of bonded atoms.

1. Polyhedral Distortion Indices. CrystalMaker now calculates distortion indicies ("DI") using the method of Baur, 1974 (Acta Cryst. B30:1195-1215). These are shown - in abbreviated form - when a fully-intact polyhedron is selected, or printed in the Output Log using the Calculate > Structure Report > Polyhedral Distortion Indices command.

   Three sets of distortion indices are reported:

   • DI (T–X) - bond distances between the centroid (T) and vertex atoms (X)

   • DI (X–T–X) - angles between shared-edge vertex atoms (X) and the centroid (T)

   • DI (X–X) - edge lengths

2. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • The Distance Explorer window's integrated toolbar now includes its structure's title.

   • Following yet more, undocumented, changes to VASP output files, CrystalMaker now adopts a more cautious approach to file loading. When an indeterminate file structure is detected, any further attempts at loading data are immediately aborted, leaving the first structure visible.

1. Cartesian Coordinates Imported from CIF files. CrystalMaker can now read orthogonal coordinates from a CIF file, as saved with the _atom_site_Cartn_x, _atom_site_Cartn_y and _atom_site_Cartn_z tags.

   Note that, as per the official CIF specifications, an orientation matrix must be specified: using the _atom_sites_fract_tran_matrix_ij tags (and optionally a translation vector, saved with the _atom_sites_Cartn_tran_vector_i tag).

   In the absence of a transformation matrix, it is impossible to relate any lattice periodicity to the (isolated) collection of orthogonal coordinates supplied: we simply cannot "second guess" the author's intentions here, or any implied axial relationships. If it isn't in the file, it doesn't exist!

   In the absence of an orientation matrix, CrystalMaker will display a warning and then do the only sensible thing: showing the atoms as an isolated "molecule".

2. Flexible VASP Trajectory Support. CrystalMaker can now handle VASP "XDATCAR" files which contain separate cell parameters for each frame. This appears to be a recent - and undocumented - 'feature' of newer versions of VASP, allowing for variations in the unit cell size/shape during refinement (previous XDATCAR files maintained the same, global, cell parameters for all frames).

3. Smaller TIFF File Output. CrystalMaker now uses the LZW compression option in its TIFF image output. This greatly reduces file size (e.g., from 108 to 1.5 MB in a typical high-resolution example).

4. Zeolite Frameworks. Added 230 ideal zeolite framework structures to the "Teaching" category of the Structures Library.

5. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • Added the Linear 3 potential, to improve relaxation of molecules containing the cyanide (-C≡N), isocyanide (-N≡C) and alkyne (-C≡C-) groups.

   • Closing a document window now causes any detached popovers (e.g., Rotator, Range, Cluster...) to be closed.

   • Opening an existing CMDX document no longer marks the document as having been edited, meaning that an otherwise unmodified document can be closed without being pestered to save it.

   • Fixed an issue reading SYSTRE files with a 'P 1' space group symbol.

   • Modified error handling for CIF files with invalid or corrupted sites. Previously, CrystalMaker would report an error for each and every invalid site - which could become tiresome for larger structures. Now, the import is abandoned after the first invalid site alert.

1. Redesigned Distance Explorer. The Distance Explorer has a sleek new design, with an elegant tool strip replacing the former "Inspector" pane, and an always-visible Sidebar offering easy customization of distance searches. The window uses Apple's new "integrated" toolbar design and features a tabbed selector button to switch between a conventional distance display, and a new Pair Distribution Function capability (see below).

   • The option to "remove duplicate distances" has been removed, as this is now performed automatically, based on whether or not the window is in "Pair Distribution Function" mode.

   • Increasing or decreasing the distance limit is now much faster, as the program is able to retain its existing distance data and merely calculate distances in an expanded range interval.

   • The graph now shows the y-value(s) at the current cursor position.

   As with earlier versions of the program, tabulated distances can be viewed in a retractable Table view, and graphics can be dragged-and-dropped into other programs, or exported via the toolbar's Output button.

2. Pair Distribution Functions. CrystalMaker can now calculate full x-ray and neutron pair distribution functions - G ( r ) - as well as “partial” P.D.F.s - g_mn( r ) - for specific element pairs. This functionality is accessed via the Pair Distribution Function tab of the revised Distance Explorer window.

   When switching to PDF mode, CrystalMaker will automatically generate the requisite range of atoms and ensure that all potential element pair combinations are searched (including "duplicate" pairs such as A → B and B → A, as required under the definition of the PDF).

   Also in PDF mode, the Search sidebar changes to allow selection of either "full" or "partial" functions. In the latter mode, a list of all potential element-pairs is enabled, permitting selection of individual "partial" PDFs.

   • Full, neutron P.D.F.s are calculated using the same tabulated nuclear scattering lengths as used in our CrystalDiffract and SingleCrystal programs.

   • Full, x-ray P.D.F.s are calculated using the atomic numbers of any elements.

   • Note that partial PDFs are dimensionless, do not incorporate scattering terms, and will appear the same regardless of which radiation type is selected.

3. Faster Synchronization. A new Sync button is available, and can be added to the toolbar via the Customize Toolbar... command. Clicking this button brings up the usual Synchronize sheet, but holding down the shift key bypasses the sheet and allow you to quickly apply the last-set options to all structures in your document. If you regularly find yourself making changes to sequences and needing to re-synchronize, this shift-click technique should prove convenient.

4. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • Updated the CrystalMaker User's Guide with a detailed description of Pair Distribution Functions and how they are calculated (see Chapter 12: Measurement). Also updated documentation regarding the new Use Auto Scale checkbox in the Range popover.

   • CrystalMaker can now deal with rogue "PDB" files generated by certain third-party simulation programs (which will remain nameless). These files - touted as being in the PDB format - lack any space group or symmetry information, and hence violate the strict PDB formatting rules. When faced with such a file, CrystalMaker will warn the user that the file is not syntactically valid, and offer to apply a default 'P 1' space group and display any data.

1. More-robust XYZ import. The program is better equipped to handle rogue text files which are not in compliance with the expected XYZ file format (but which still use the ".xyz" file extension).

   Update: 15 November 2021 - the import process now ignores any (syntactically-invalid) blank lines at the end of a file, which would otherwise cause the import to fail.

2. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • Spurious console log errors relating to update checking are now suppressed.

   • Updated the licence verification procedure to cope with expiry dates from 2024 and beyond.

1. Plot Range Auto Scale Option. The Range popover now includes an "Auto Scale" checkbox. This is enabled by default, meaning that the structure will be rescaled to fit inside the graphics pane in any orientation. However, you can now disable this setting, which allows you to preserve the scale when making range adjustments.

   This will be particularly useful when viewing a structure along its long dimension, and adjusting the range perpendicular to this dimension; no longer will the structure appear to shrink when comparatively minor adjustments are made.

2. Changed Scaling Behaviour for Isolate/Hide commands. The following commands no longer automatically reset the scale:-

   • Isolate Selection
   • Isolate Selected Molecules
   • Isolate Selected Fragments
   • Hide Fragments

   This change should help improve continuity when making subtle changes to a structure. (Users can always click the toolbar's Auto Scale button if re-scaling is required.)

3. Multi-Touch Volumetric Threshold Slider. When adjusting the minimum and maximum thresholds for volumetric datasets, you can now use multi touch. Simply position your mouse pointer over one of the two slider "thumbs", then gently slide two fingers to the left or right, across your trackpad. The slider thumb nearest to the mouse responds.

   This allows a smoother and more precise adjustment of the thresholds, compared to clicking-and-dragging the mouse.

4. Licence Expiry Warning. For expiring licences, a warning message is now shown close to the expiry date. This appears once a week for three weeks, and then daily.

5. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • Rendering volumetric datasets as iso-surfaces or iso-volumes is now ca. 2x faster.

   • The Check for Update command is now available when running in "Demo Mode".

   • Fixed a rare issue with the rendering of "two tone" bond cylinders, which could see the colours reversed.

   • Fixed a memory leak associated with changing the threshold(s) for displaying volumetric datasets.

   • Fixed an issue in which sliced volumetric datasets - rendered as "iso volumes" could show incorrect or random colouring.

1. Extended Bond Distance Output. When using the Bond Distance Tool to measure distances between atoms in two different structures, CrystalMaker now prints extended information in the Output Log. In addition to the actual 3D distance and the projected distance (in the plane of the screen), CrystalMaker also lists the vector components, parallel to the (orthogonal) screen axes.

   This information might be useful when attempting to align different structures; the vector displacement can be entered into the Transform > Scale & Centre > Move Structures command, to move one (unlocked) structure relative to another (locked or hidden) structure.

2. Improved "Labels to Textboxes" command. This command used to require that individual atoms be selected, in order to convert their labels into text boxes. That was perhaps not very intuitive, and resulted in the command typically being greyed out (inactive). We have now changed the behaviour of the command, such that any visible atom labels are now converted into text boxes. This should make the command more accessible.

3. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • The Licence command in the "About" window is no longer modal, and can be closed without having to (re-)accept the licensing agreement.

   • Added a workaround for an issue on macOS 10.6.1 and later, in which certain interface elements (e.g., the Unit Cell group in the Model Inspector) were not correctly enabled. This appears to be an underlying system issue, as earlier versions of macOS show the correct behaviour. Regardless, our workaround should ensure reliable behaviour on all versions of macOS.

1. Visualize Disordered Sites. This major new feature has been added to the Transform menu, allowing visualization of substitutional disorder in crystals.

   The new Transform > Visualize Disordered Sites command is active for crystal structures which include some degree of site disorder and/or vacancies. The command prompts for a multiplicity factor, then proceeds to generate a new structure - generally a supercell - with a random distribution of any disordered site occupants and/or vacancies.

   This new command may be useful for teaching purposes, in revealing disordered distributions graphically (the larger the supercell, the better) - and potentially also in preparing input for modelling programs, which require specific atoms at specific positions in a unit cell.

   As part of the new command, CrystalMaker calculates the minimum supercell size (multiplicity factor) required to show at least one atom of the least-common site occupant (occupants and vacancies with site fractions less than 0.001 are ignored). Note that, in general, higher multiplicities will give a closer approximation to the original formula, as well as a more "random" looking distribution.

   For more information about using this new command, please refer to the updated Online Help, User's Guide, and Video Tutorials.

2. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • The Transform > Unit Cell commands are now faster, thanks to performance optimizations.

   • Fixed a display issue on macOS "Big Sur" with Structures List thumbnail titles not centred correctly.

   • Changing the plot range now correctly updates the depth fading of atoms.

1. Major Online Help Refresh. The online help system has been given a major refresh, with a new visual design, as well as substantial rewriting.

2. Blank Site Label Detection. This version will automatically fix any blank site labels detected during the import of a CMDX document (which might otherwise cause a crash). The crystal editor has also been upgraded to prevent the definition of blank site labels.

3. Miscellaneous. This version includes miscellaneous fixes and enhancements.

   • Fixed a rare issue in the Distance Explorer, where histogram bar heights could subtly change between measurements, because of multi-threading issues.

1. Improved File Export Options. The File > Export Data submenu has been improved, both in terms of layout and command names. Submenus are now used to group related commands, e.g., a new Coordination Environments submenu gives access to the former Visible Coordination and Crystal Coordination commands; and a new PDB submenu give a choice of "molecule" or "crystal" export. The "HTML Structure Report" command has now been renamed as "HTML", and grouped with other external formats.

2. Improved XYZ Export. When choosing to export XYZ data, earlier versions of CrystalMaker X exported all structures loaded in the current document, regardless of visibility. Some users found this confusing, so we have now added the option to only export visible structures to an XYZ file. This option - and the "all structures" option are now accessed via a new File > Export Data > XYZ submenu.

3. Miscellaneous. This version includes workarounds for Apple bugs affecting M1 processors and "Big Sur"; we also include miscellaneous fixes and enhancements.

   • Workaround for Apple graphics bug on M1 processors: bonds were being displayed in red or black. This issue has been reported to Apple; in the meantime, we have devised a workaround.

   • When importing volumetric data from CUBE, Voxel or GRD formats, the user's preferred display style (as defined in the Preferences panel) is applied to the resulting visualizations.

   • Improved licensing agreement viewer (as accessed via the Licence button in the "About" window. This no longer requires users to explicitly "agree" or "disagree" when merely reviewing the content.

   • "Sliding sidebars" now animate correctly on macOS 11 "Big Sur".

   • Fixed a problem with exporting stereo-pair graphics at very-high resolution which resulted in an interleaved series of images instead of a seamless view.

   • Fixed an issue with the Discard Symmetry command; new atoms are now immediately generated corresponding to the increased number of sites in the asymmetric unit.

   • Workarounds for popup menus in Big Sur. Changed system behaviour led to titles being shown clipped.

   • Fixed a potential issue with entering blank values into the Supercell sheet data fields; zeroes are now used in these cases.

   • This version includes additional stability improvements and integrity checks to ensure safe operation.

1. Universal Binary. CrystalMaker 10.6 runs natively on Apple Silicon! The same application also runs natively on older, Intel-based Macs: it is distributed as a "Universal Binary", to give you maximum flexibility - and performance.

2. Improved Discard Symmetry. The Transform > Discard Symmetry command now uses symmetry operators to convert anisotropic displacement parameters and errors in fractional coordinates - for all newly-created sites in the expanded asymmetric unit.

3. Improved "Big Sur" appearance. Extensive updates have been made to the user interface to ensure a consistent look under macOS 11.x "Big Sur". This includes larger popup menus in the toolbar and narrower inspector lists. The Distance-, Vibration- and Symmetry Explorer windows now have an "integrated" toolbar design, with resized toolbar button icons. The Preferences Panel now shows a standard "Preferences" toolbar appearance. Sliders have been reset to ensure their thumbs aren't cropped.

4. Miscellaneous. This version includes miscellaneous enhancements and fixes.

   • The Structures List and Inspector are now animated so that they slide in- and out of view.

   • The View submenus now allow toggling of the Structures List and Inspector list.

   • The Tool Strip now shows a diffuse background on "Big Sur".

   • Improved update checking algorithm with more modern design and efficient operation.

   • Window playback control icons are now visible on "Big Sur".

1. Ready for Big Sur! This version includes a number of workarounds to ensure optimum display on macOS 11 "Big Sur". This includes fixes for background and bond previews, changes in font metrics and, critically, improvements to thumbnail display in the Sidebar, to account for the new list display in "Big Sur".

2. Reset Molecular Coordinates. A new Transform > Reset Molecular Coordinates command allows molecular structures to have their atomic coordinates reset so that they apply to the current screen axes (rather than an initial axial set when the structure was first created or imported).

3. Miscellaneous. This version includes miscellaneous enhancements and fixes.

   • Fixed a bug with the display of dashed lines in polyhedra when perspective is enabled. Dashes could be drawn at the edges of the polyhedra, rather than inside the polyhedron.

   • Fixed a rare issue with loading non-conventional element symbols from CIF files. Unconventional element symbols (such as "Va") were converted to the closest-equivalent element symbol (e.g., "V"), which was not what some users were expecting. We now preserve these element symbols.

   • Atomic radii set using the Selection Inspector can now be larger than 10 Å.

1. New Van-der-Waals Radii. This version of CrystalMaker includes a fully-revised set of van-der-Waals radii, using recent data published by Prof Santiago Alvarez (and others). This provides a vastly-more comprehensive coverage, with more-accurate values.

2. New Bond Range Generation for Text Files. CrystalMaker text files (CMTX) can now include new "BRNG" cards which specify automatic bond (and hence polyhedra) generation between a specified pair of element symbols, within the specified distance range. Such cards provide a more-precise alternative to the existing "BOND" or "BMAX" cards.

   Please see Appendix B: CrystalMaker Text Format in the CrystalMaker User's Guide for more details.

3. Miscellaneous. This version includes miscellaneous enhancements and fixes.

   • Added a workaround for incomplete (and technically, invalid) AXSF files. Any invalid structures are now skipped, allowing the program to load remaining (valid) structures. Error messages also now include line numbers for easier self-diagnosis.

   • CrystalMaker can now parse CMTX files with NOTE lines containing fewer than four characters, and should correctly respect any "hard returns" inserted within the text.

   • Fixed a rare issue with Stick plots that use thin bond styles; the "elbow joints" connecting thin sticks were drawn at the wrong radii.

   • An extremely-rare bug with the display of near-vertical bond cylinders has been resolved.

   • The window Ruler is now automatically updated when entering an explicit scale via the Set Scale command.

   • Fixed a rare issue with dashed lines occasionally being drawn at the edge of a polyhedron (rather than only being shown for occluded rear edges). The issue was related to a mismatch between the geometric centroid of the polyhedron, and the location of its host atom.

1. Enhanced Precision for Hexagonal Cells. CrystalMaker will now, by default, identify special positions in crystals with hexagonal lattices and enhance their precision. The sites in question correspond to x or y values with fractional coordinates close to 1/6, 1/3, 2/3 or 5/6. CrystalMaker's existing 64-bit precision means that even sites entered using four decimal places (e.g., "0.3333") will result in the display of "split sites", which is undesirable in the majority of cases. The new scheme will intercept such positions and replace their coordinates with their fractional equivalents.

   This option can be disabled using a new "Enhance precision" checkbox in the General pane of the Preferences panel. Please note also that any sites entered with less than four decimal places (e.g., "0.333") will be treated as intentional, and won't be offset to the nearest fractional (1/3) value.

2. Improved SYSTRE File Import. SYSTRE files - which are designed to show symmetry-related framework topologies - are now imported without inserting dummy edge atoms. Instead, CrystalMaker uses its in-built symmetry-related bond detection, applying appropriate colouring to individual bonds in the framework.

   CrystalMaker will pre-generate an extended range of lattice, allowing users to expand the plot range and still retain symmetry-related bonding colouring. However, please note that massive range changes will reset bond colouring to default values.

3. Miscellaneous. This version includes miscellaneous enhancements and fixes.

   • The default surface opacity has been increased from 0.4 to 0.95 to make the surface easier to see, whilst still allowing a (subtle) peek of the structure inside.

   • Fixed an auto-scaling issue with volumetric data. If no atoms or unit cell frame were visible, the Auto Scale command caused voxels to vanish.

   • Dragging-and-dropping a structure thumbnail into another window now correctly transfers surface type and colour information.

   • Improved the way in which selected sites are merged in a crystal, as part of the Merge command. Sites with the same fractional coordinates but different site occupants now use the colour and radius settings for the dominant element.

   • Fixed a problem importing VASP volumetric data which had required the user to reset the plot range in order to see any datasets.

   • Fixed a cosmetic issue with zero indices appearing occasionally when setting the view direction. This (rare) issue occurred when attempting to display rational indices, with the resulting large numbers overflowing the display space.

1. Batch Molecular Relaxation. It is now possible to queue a list of molecular structures for relaxation. To accomplish this, one simply needs to load all structures into the same document's Structures List and then choose the new Transform > Relax All Molecules command. (This is a dynamical menu command: hold down the shift key to change Relax Molecules to Relax All Molecules.) You can also shift-click the Relax button in the toolbar.

   Once batch relaxation is underway, a progress bar is shown, with a Cancel button.

2. Improved Polyhedral Face Display. It is now possible to specify highly-distorted "faces" to be shown as single, smooth, concave faces - without these being further subdivided into separate polygonal elements. This allows, for example, the depiction of CaO₈ units in Andradite (garnet) as distorted cubes. It also means that the existing polyhedral edges can be emphasized, rather than having to superimpose inter-atomic bonds as faux polyhedral edges.

   To take advantage of the new algorithm, use the Polyhedral group in the Model Inspector, click the Face button and use its popover to increase the out-of-plane tolerance to (say) 0.5 Å. For best results, we also recommend clicking the Geometry popup and choosing: Allow Concave.

3. Miscellaneous. This version includes miscellaneous enhancements and fixes.

   • Longer atom vectors can now be defined. Earlier versions had a maximum 10 Å limit, which now been removed.

   • Added a new tool strip preference to disable the "blurred background" effect. On some, older, machines the blurring effect (which uses Apple's Core Animation) can give rise to unwanted distortion and colour flicker.

   • Removed the (disabled) "Relax Slab" command from the Transform menu.

   • Resolve a situation where extremely-distorted polyhedra sometimes had missing segments.

   • Anion-anion bonds are again generated as part of the Auto-Bonding algorithm.

   • Added a workaround for a system issue (on some, but not all, Macs) which could cause a program hang when adding multiple structures to the Structures List.

     The issue was related to the way in which the operating system then displayed a vertical scroll bar. Normally, this should appear as an overlay, but on the affected machines it was actually resizing the embedded list. This caused an infinite sequence: showing the scroll bar made the list narrower and shorter - thereby causing the scroll bar to vanish; this caused the list to become wider and taller, making the scroll bar reappear - and so on, ad infinitum.

   • This version includes optimizations to improve multi-threaded operations and avoid (rare) deadlock conditions.

This version includes minor fixes and workarounds for a system issue detected after the main 10.5 update.

• The Add Atom tool can now be used to add new atoms and bonds for crystals. Holding down the shift key between mouse clicks now successfully adds bonds between the clicked atoms.

• The File > Export Data > Visible Coordination command now gives neater formatted output for molecules.

• This version includes a workaround to address a memory-locking issue encountered when reading from XYZ files.

• The Calculate > Single-Crystal Diffraction commands now work correctly, even if SingleCrystal 4 is not running.

This version is no longer compatible with the Leap Motion 3D Controller - see note below.

1. Works with SingleCrystal 4. The single-crystal diffraction commands now work with the all-new 64-bit SingleCrystal 4. This includes the existing "Live Rotation Mode", as well as new commands to Add and Replace diffraction patterns.

   Please note: for these commands to work you will need to have installed SingleCrystal 4 in your Applications folder - and unlocked that application. These commands do not work in "Demonstration Mode" for either application.

2. Live Intensity Mode with SingleCrystal 4. Users with the full-feature version of SingleCrystal 4 can now take advantage of a new, "Live Intensity" mode with CrystalMaker. When this mode is enabled, via CrystalMaker's Calculate > Single-Crystal Diffraction > Enable Live Intensities command, then any changes made to the crystal structure in CrystalMaker will cause the corresponding single-crystal diffraction pattern in SingleCrystal 4 to be updated. For example, you might select one or more atoms in CrystalMaker, move or rotate them, change their occupancies - or event animate a phase transition - and whilst this is happening, the simulated single-crystal diffraction pattern will be updated live.

3. SYSTRE File Import. CrystalMaker can now read from SYSTRE data files and show symmetry-related bonding topologies.

   SYSTRE is a "Java" program for analysing periodic nets in crystal structures. CrystalMaker can read from its Structure File format (file extension ".cgd") and will show symmetry-related bonds in the structure using colour coding. As connectivity is the raison d'etre of this format, a default "stick" model type is automatically applied.

   Because CrystalMaker's bond generation algorithm is based on element-pair/distance combinations, the program has to undertake some additional steps in order to propagate symmetry-related bonds throughout an extended structure. This involves the insertion of "dummy" atoms at the centre of each bond, with unique element symbols.

4. Calculate Distance Between Planes. Whilst CrystalMaker can easily calculate the d-spacing for any set of lattice planes (via the D-Spacing Calculator), it was not possible to directly calculate the instantaneous distance between two lattice planes displayed on screen. In this version, we have added a new Calculate > Distance Between Planes command, which calculates the perpendicular distance between two parallel lattice planes.

   To use this command, use the Lattice Planes group in the Volume Inspector to add two parallel planes to the structure; you can move the planes relative to each other, and then use this command to calculate their separation.

5. Export Vibrational Spectra. You can now export simulated vibrational spectra to a text file by right-clicking in the Vibrations Explorer graph and choosing Export Data from the contextual menu that appears.

6. Miscellaneous. This version includes improved "pie-chart" spheres, improved user interface design and minor fixes.

   • Pie-chart spheres can now show up to eight coloured sectors (instead of four).

   • The Legend and Tool Strip now provide haptic feedback when "snapping" into position on the screen.

   • Segmented buttons in the window toolbar now have Help tips (requires macOS 10.13 or later).

   • Improved the Transform > Unit Cell menu icons. These are now easier to read in "Dark Mode".

   • Added a New Window command to the program's Dock menu. This allows you to create a new document from any "Space", without having to bring an existing window to the front (and risk changing the active space as a result).

   • The File > Open File with Format command has been renamed as Open with Format.

   • The Library viewer's left/right ions have been redesigned to make them more distinctive on a variety of different backgrounds.

   • In "Demo Mode", Library window folders and sub-folders are now sorted correctly.

   • Improved VASP import: the program can now cope with blank lines at the end of POSCAR files, and between different datasets in multi-structure files.

   • Improved STL 3D output: fixed a bug that caused gaps to appear between some coordination polyhedra.

   • Improved "Demo" alert, with a clearer layout and an attractive Help & Tutorials popover.

1. Workarounds for Apple Multi-Threading Bug. The latest system updates for macOS 10.15 "Catalina" and 10.14 "Mojave" include changes to the way in which multiple application threads are marshalled by the system. Such "multi-threading" had been used to used to accelerate the data conversion and import from our legacy "CMDF" file format - but under the new systems, multiple threads become deadlocked, with the result that the program appears to "hang", with no progress.

   This version avoids using multi-threading in this particular context, which ensures that legacy files can be imported without issue (albeit with slightly lower performance). Please note that our extensive use of multi-threading in other areas of the program is not affected.

2. Miscellaneous. This version includes a more robust symmetry-detection algorithm plus minor fixes.

   • In response to new Apple guidelines, this version includes more-robust background processing, designed to ensure safe running under "Catalina" and future releases.

   • A rare issue that prevented space group symmetry from being correctly detected has now been resolved. The issue involved certain space groups with origin offsets - as recorded in their general equivalent positions.

   • Attempting to edit a bond colour (using the Bonds Inspector) no longer causes a crash on macOS 10.15 "Catalina".

1. Workarounds for Bugs in Catalina. This version includes important workarounds for bugs in macOS 10.15 "Catalina" - specifically, a window flicking (an issue in Core Animation with Xcode 11) and garbled text on some machines (an inconsistency in a system pixel map function).

   These bugs have been reported to Apple, but our workarounds mean we don't have to wait for any official bug fixes.

2. Notarized Application. In addition to being "code signed", this version is officially "notarized" by Apple - meaning it can be run (without workarounds) when downloaded onto a Mac running "Catalina".

3. New Symmetry-Related Bonds Algorithm. A new algorithm has been developed for selecting symmetry-related bonds. Whereas the old algorithm selected bonds whose site atoms matched, the new algorithm generates intermediate points along each bond and uses symmetry to match the corresponding points in other locations inside the unit cell. This gives a more-rigorous interpretation and makes working with inter-penetrating lattices (amongst others) easier.

4. Miscellaneous. This version includes miscellaneous enhancements and fixes.

   • Massive CIFs are now much faster to import.

   • CIFs that use space-group numbers no longer cause a "missing space group" warning.

   • DL_POLY "History" files now use unique names for the different structures loaded. Also, "History" files that contain only a single structure, can again be imported.

   • GROMACS files which contain 5-digit atom numbers are now read correctly.

   • When importing a text file, the site-labelling algorithm can now cope if an element symbol is in upper case.

   • This version now recognises the new "e-glide" convention, as used in space groups 39, 41, 64, 67 and 68.

   • This version supports licence codes with higher-value (> 4000) serial numbers.

   • Occasional problems associated with closing a document window on Mac OS X 10.10 - 10.12 have been resolved.

   • Fixed issues with centred atom labels not appearing correctly (this was an issue on systems using Intel Integrated Graphics).

1. Vertical Layout Option. The Output Log pane can now be toggled between the usual, horizontal layout, or a new, vertical layout. The latter is useful when browsing extensive data listings.

   To switch between the two layouts one can either use new View > Output Log submenu, or use the Rotate button in the Output Log header (rotate icon).

2. Searchable Output Log. A new Search field has been added to the Output Log's header, allowing easy search: simply enter a search string and press the Return key; continue pressing this key to find subsequent occurrences of the string.

   The Output Log header also includes a close button and a rotate button (toggling between horizontal or vertical layouts).

3. Improved Text Import. CrystalMaker now offers smarter loading of "custom" atom labels - as read from CASTEP, GULP and other text formats. Element symbols can now be correctly read from labels that combine an element symbol and a numeric part, e.g., "Si27". (In earlier versions of the software, it was assumed that the atom label consisted purely of an element symbol, resulting in unrecognized symbols being loaded, and as a result, "grey" atoms being plotted.)

4. Miscellaneous. This version includes miscellaneous fixes.

   • Distances and Angles output (screen and to file) now includes the volume of each polyhedral site, together with a summary of the number of faces, sorted by the number of vertices.

   • Moving the mouse over the Structures List header causes a drop-down menu indicator to appear. Clicking this provides easy access to the contextual menu commands.

   • The default toolbar layout now includes the Log button.

   • Added a workaround for a system-related issue with the rendering of COLLADA files where perspective has been defined.

   • Fixed an issue with the interpretation of origin offsets loaded from CASTEP files.

1. Faster Hide Stranded Atoms. The Hide Stranded Atoms command is now considerably faster (over 8× faster in our tests), thanks to faster memory access and an optimized algorithm.

2. Improved Merge Sites Option. It is now possible to merge all sites whose atoms lie within a specified distance. This option is available currently via the Transform > Unit Cell > Collapse Supercell command - the difference being that one can now specify a regular cell (1 × 1 × 1) instead of a supercell.

   An additional improvement is that this command now executes a series of cycles, resulting in more effective merging of close sites.

3. Help & Tutorials. A new popover button has been added to the "Demo" and "Registration windows, providing direct access to the Tutorials, User's Guide and Video Tour. The displayed popover also emphasizes the fact that full-featured support is already included within the program, does not need to be separately downloaded, and is readily accessed via a handy "Help" menu (!).

4. Miscellaneous. This version includes miscellaneous fixes.

   • Fixed a very-rare issue with bond generation for massive structures. A multi-processing timing issue could result in the resetting of coordination data, which then curtailed subsequent bond searches. These issues have now been resolved.

   • The Cluster popover now correctly updates its "combo box" each time the popover is shown.

   • The Info Inspector now correctly shows angles for triclinic crystals.

   • Added a special workaround to allow non-standard DL_POLY "HISTORY" files to be loaded. Such files deviate from the file format by having different numbers of atoms in each structure, contrary to the file header instructions.

   • The Calculate > Angle Info command now correctly shows angular information, rather than coordination data.

   • Crystal Coordination output files now correctly include all sites.

   • Added a workaround to a system issue which prevented the Preferences panel from opening correctly on macOS version 10.10 - 10.12.

   • A minor, cosmetic issue with Library thumbnails and their "info" buttons has been addressed.

   • Fixed a rare bug with the Add Atom tool which only happened if all atoms were deleted and a new atom subsequently added.

1. Animation Playback Controls. A new View > Playback Controls menu command displays a floating window with controls for playing an animation, changing the frame rate, setting its synchronization options, jumping to the first or last frame, or stepping forward or backwards.

   Perhaps the most-important feature of the Playback Controls is a new "scrubber" bar. This lets you rapidly scan through extended multi-frame structure sequences/trajectories.

   This floating window replaces the old "Animation Popover" (accessed by clicking-and-holding the Play button in the window toolbar).

2. Imports VASP "XDATCAR" Trajectory Files. CrystalMaker can now import VASP trajectory files in its "XDATCAR" format. Such files should either be named "XDATCAR", or should have the ".vasp" file extension.

3. Multi-Structure Files Load Significantly Faster. Major optimizations have been made, allowing multi-structure text files to be loaded considerably faster than before - a factor of 10 in some cases!

   For example:

   • A 225 MB DL_POLY "History" file containing 1001 structures (each with 1536 atoms) was loaded in just 9 s, compared with 90 s before (10× faster).

   • A 48 MB "XYZ" file comprising 1452 structures (each with 1000 atoms) was loaded in just 8 s, compared with 60 s before (7.5× faster).

   (Measurements made on a 4 GHz Intel Core i7 iMac, with automatic bond generation turned off.)

   Note that a (small) part of the speed improvement relates to a smaller initial atom range for crystals, showing the contents of one unit cell (i.e., 0 ≤ xyz < 1), rather than an extended range (0 ≤ xyz ≤ 1) of 2 × 2 × 2 cells. This range change only applies when reading crystal trajectory formats such as DL_POLY/HISTORY and VASP/XDATCAR.

4. Improved, Faster Animation. The new Playback Controls window allows an arbitrary animation speed, with presets for faster speeds (50, 100, 200 fps). At higher speeds, the program will now automatically drop frames (if required) to ensure the display keeps up with the requested frame rate.

   When starting an animation, the scale of the first "frame" is now automatically applied to all other frames - if the Synchronize Scale option is set.

   When loading a "trajectory" from formats such as VASP, XYZ, DL_POLY, CASTEP, LAMMPS, XSF, GROMACS or DMol3, a consistent plot centre is automatically applied. This, and the synchronized scale previously mentioned, means that animations can now be made without any annoying "wiggling" between structures.

5. Miscellaneous. This version includes miscellaneous optimizations and bug fixes.

   • New "Heat" gradient available for volumetric datasets.

   • Added the ability to set the view direction parallel to any selected bond or atom vector.

   • Changed keyboard shortcut: command-option-B now corresponds to: Transform > Auto-Generate Bonds. (Formerly, this shortcut was used to show the Library window.)

   • GROMACS and CASTEP multi-structure import now makes the first structure visible, rather than the last one!

   • Toggling the Grid now applies to all structures in an animation.

   • Axial vectors are now correctly shown during animation.

   • XYZ files with atom labels containing symbols plus numbers can now be correctly read into the program.

   • Atom serial numbers, as imported from a PDB file, are now faithfully reproduced. Earlier versions of the program interpreted these numbers as being in hexadecimal format (required for larger PDB file), whereas many structures using integer format.

   • Fixed a rare bug with the Bond Distance tool. When working with atoms in different structures, clicking on the second atom to lock the measurement resulted in the wrong distance being shown on the screen (although the Log output was correct).

   • Fixed a bug (introduced in the previous version) when exporting a crystal structure to a molecular format such as XYZ. Incorrect z-coordinates were being written.

1. Calculate Angle Between Molecules. A new Calculate > Angle Between Molecules command has been added. This automates the process of:-

   1. Extending exiting selections to their entire molecules.

   2. Calculating the best-fit plane through each of the two molecules.

   3. Measuring the angle between the two best-fit planes.

   To measure the angle between two molecules, one simply needs to select one atom in each molecule, then execute the new menu command. The included angle is displayed in the document's Log pane, together with the best-fit planes for each molecule.

2. Improved XYZ, Chem3D, PDB & DMol3 Output. CrystalMaker now seeks to preserve the orthogonal structural coordinates when exporting data to "molecular" formats such as XYZ and PDB.

   Whilst, ideally, third-party programs would be smart enough to deal with proper crystallographic axes, sadly this does not seem to be the case. A number of popularly-used programs seem focused exclusively on molecular structures and are entirely reliant on the use of orthogonal coordinates...

   Previous versions of CrystalMaker used the screen coordinates for file export - but these change as the structure is rotated, making it harder to pin down axial orientations in non-crystallographic third-party software. Hence, in this version of CrystalMaker, we now maintain rotation-independent coordinates for use during file export.

   If you had previously imported your structure with a set of orthogonal coordinates, then this axial system is preserved. If you generated an output file from a crystal structure, then CrystalMaker now uses the standard axial convention:-

   • The ortho x-axis is parallel to the crystal x-axis.

   • The ortho y-axis lies in the crystal's xy plane and is perpendicular to the x-axis.

   • The ortho z-axis is perpendicular to both the ortho x- and y-axes.

3. PDB Molecule Export Option. When working with a crystal structure, you now have the choice of exporting a PDB file either as a "molecule" (which includes all visible atoms and their connectivity) - or as a "crystal" (which includes the full contents of the unit cell, but no connectivity data). These options are present on the File > Export Data submenu.

4. Expanded Structures Library. We have added 17 new structures to the Reference collection. These include topical phases such as polymorphs of CsPbI₃. The Teaching collection now includes elegant new multi-structure presentations of BCC, CCP and HCP phases - ideal for use in teaching classes. We have also added folder notes to all Basic Structure Types subfolders.

   The Examples collection also includes a new "CCP + BCC Intergrowth" file: this multi-structure file provides a step-by-step guide to creating - and topotactically matching - two different structures, which are then merged to produce a crystal supercell.

5. Miscellaneous. This version includes miscellaneous optimizations and bug fixes.

   • Improved Library Browser navigation: You can now use a multi-touch three-finger "swipe" gesture to move backwards or forwards through your navigation hierarchy.

   • The Tidy popover now includes a Hide Fragments button.

   • The User's Guide and the Self-Guided Tutorials have been updated to emphasize that many of our popovers can be detached.

   • Improved atom vector display. The "From Atom" style now starts at the centre of its host atom, meaning that this style works well for translucent or blank styles.

   • VESTA files with blank thermal ellipsoid tensors can now be imported safely.

1. Collapse Supercell. A new unit cell transformation has been added to the Transform > Unit Cell submenu. The Collapse Supercell command allows you to reduce a supercell to its subunit size, with the option of merging all same-element sites within a specified distance range.

   For example, consider an 8 × 12 × 12 supercell, created using CrystalMaker and then exported into a modelling program. After running a modelling calculation, atoms will have moved from their starting positions, so that upon collapsing the supercell, multiple atoms (from different parts of the supercell) will be "wrapped" onto similar positions in the subcell. CrystalMaker will assign a partial occupancy for each site. The "merge" option allows you to calculate an average structure.

2. Atom Density Map. A new volumetric calculation lets you display the density of atomic sites in a disordered structure - for example, a "collapsed" supercell.

   This visualization is similar to the existing Porosity visualization - but whereas that simply marks each volume element ("voxel") as being filled or unfilled, the Atom Density map assigns a numeric value to each voxel, based on how many atoms are intersected by the voxel. In conjunction with a Point Cloud or Lattice Plane Slice visualization, this gives a clearer indication of the actual density of sites, compared, say, to a space-filling model - in which atoms are rendered opaquely.

3. New Structure Reports. The Calculate > Structure Report submenu now includes options to generate detailed reports for coordination, crystal coordination and a "distances and angles" summary - these were previously limited to file export only, but can now be viewed in the Log pane.

4. CIF workaround for MSA Crystal Structures Database. The NSF-funded MSA crystal structures database offers a rather crude CIF export option. Site labels and their occupancies are mangled together, resulting in potential ambiguity and loss of original-author label information. CrystalMaker now attempts to reconstruct element data from the first two characters of the mangled site label, for example, choosing "K" for the site labelled "Ka" and "O" for the site labelled "Ob". Note that a "Ca" site could contain either Ca or C, however!

5. Extended Structures Library. We are continuing to update and increase the size of our structures library. As well as a number of new phases, we have correctly the (misnamed in the literature) "Omnisteinbergite" phase as "Dmnisteinbergite" and moved it to the Minerals collection.

6. Miscellaneous. This version includes miscellaneous optimizations and bug fixes.

   • When defining a cluster, the central atom is now shown selected (as for CrystalMaker 9 and earlier). This facilitates hiding that atom, or selecting its n nearest neighbours.

   • Improved Distance from Plane command: data for any hidden planes is now suppressed.

   • Changed keyboard shortcuts for the File > Save As and the (dynamical) File > Duplicate commands. The Save As command now has the shortcut: cmd-shift-S (which matches CrystalMaker 9 and earlier), whereas the (little-used?) Duplicate command has the shortcut: cmd-option-shift-S.

   • Added the (non-conventional) monoclinic space group, I 2/a.

   • CrystalMaker text files (CMTX) with the SPGR card placed before the CELL card are now correctly read.

   • Fixed an issue with the Atoms Inspector in slide-out overlay mode, where the colour buttons ceased to work.

   • Crystal Coordination file output now correctly lists all bonded neighbours.

   • When opening a document with invalid or missing font references, text is shown at the correct size, using the default font.

   • Invalid or missing file favourites are now automatically purged from the Structures Library.

   • A rare out-of-memory issue associated with the generation of CMTX files (including during diffraction simulations) has now been resolved.

   • Measurement overlays are now correctly sized on regular (non-Retina) screens without the "fast rotation mode" in effect.

   • When exporting animation movies, the scale values are now correctly set from each structure, rather than just the first structure.

   • Multi-touch thumbnail resizing now works again for the Structures Library.

   • Fixed an issue with library thumbnails for text files being generated at the wrong size.

   • A rare issue in which the use of the Repair > Bonding Around Selection command resulted in new atoms appearing in the wrong locations, has now been fixed.

1. "Dark Mode" Support for "Mojave". CrystalMaker now fully supports the new "Dark Mode" feature in macOS 10.14 "Mojave". This has entailed major interface redesign, with new application icons and revised drawing code.

   Another change is that the Tool Strip now automatically switches between light or dark modes. In "light mode", the Tool Strip detects the background brightness and will revert to a dark appearance if required.

2. Redesigned Library with CrystalViewer. The Library window has been extensively redesigned and now provides easy access to documentation, as well as custom images and PDF files - and incorporates a sleek CrystalViewer for fuss-free structure visualization.

   • The new "Documentation library" shows the self-guided (PDF) tutorial, the User's Guide, online help - plus a number of links to our website. Double-clicking on any of the icons results in the appropriate application being used to open the associated file.

   • Non-structure files, such as images and PDF documents, can now be added to the Favourites pane of the Library browser. When double-clicked, these documents will open in their default applications (e.g., "Preview").

   • A Viewer mode is available for any structure file. To activate this, you choose one of the following:-

     1. Force-click any thumbnail.

     2. Select the file then press the space key on your keyboard.

     3. Select the file then click the Preview ("i" icon) button in the toolbar.

     4. Move the mouse pointer over the file icon so that the "i" icon appears over the thumbnail, then click the icon to show the viewer.

     The resulting Viewer shows one or more auto-rotating structures and their notes. You can use the contextual menu to toggle auto-rotation on or off. You can rotate and scale the structure using the mouse or trackpad (in the same way as in a document window's Graphics pane). You can also change model type and switch to a 3D mode, using the Model menu in the main menubar.

     Moving the mouse towards the left or right of the viewer pane displays arrow buttons, letting you navigate through the files in the current browser pane.

     To exit the Viewer and return to the Browser, do one of the following:-

     1. Press the Escape key.

     2. Press the Space bar.

     3. Move the mouse pointer towards the top of the window so that the Close and Zoom buttons appear, then click the Close button.

   • A full-screen "Presentation Mode" can be accessed via the contextual menu, or via the Play button in the toolbar. In this mode, all visible structure files have their contents animated.

     To control the speed of animation (i.e., the amount of time spent on each file), click-and-hold the Play button so that a popover appears, then adjust the slider to set the time per file.

   • New "Auto Open and Close" option. This - the default option - ensures that the Library Browser is automatically closed whenever a document is opened, and reappears when the last document window is closed. In this way, the window provides a springboard to your structures, and keeps out of the way when not required.

     If you wish to keep the Library Browser open all the time, simply turn this option off in the General pane of the Preferences panel.

   • Automatic saving of Library Browser position, size, selection and other settings.

   • Folder Notes are now displayed above the thumbnails in the Library Browser. These are designed to be informative and we hope they will be useful in teaching. To hide the folder notes, move the mouse over the note so that a close icon, then click this.

3. New Modelling Engine. The energy-modelling code has been exhaustively refreshed, resulting in much better performance - and reliability. Torsions are now correctly accounted for, rings are automatically detected and many new potentials added. Performance is greatly improved - especially for the Add Hydrogens command.

4. Live Powder Diffraction. A new "Live" powder diffraction mode allows you to directly relate changes in your crystal structure to its diffraction properties. Choosing the new Calculate > Powder Diffraction > Enable Live Diffraction command establishes a link between the current CrystalMaker window and the frontmost window in CrystalDiffract. Thereafter, any changes you make to the primary-selected structure in CrystalMaker will trigger an update of the frontmost diffraction pattern in CrystalDiffract.

   As an example, you might want to see what happens when you rotate a group of atoms in the unit cell; you will see the corresponding powder diffraction pattern update in real time. Alternatively, you might animate a sequence of structures—perhaps spanning a displacive phase transition—and then be able to observe powder diffraction peaks splitting. Either way, this is a much-clearer way of understanding the relationship between a crystal structure and its powder diffraction properties. We encourage you to experiment!

   In addition to the "Live Powder Diffraction" mode, two new options have been added for simulating powder diffraction patterns via CrystalMaker:-

   • New Pattern. This command adds a new pattern to the frontmost window in CrystalDiffract. (It replaces the old Powder Diffaction command, with the difference that instead of a new window being opened up each time, a new pattern is added to the same CrystalDiffract window. If you require a new window, simply open a blank document in CrystalDiffract, and new patterns will be added to this.)

   • Replace Pattern. This command - which has the keyboard shortcut: cmd-shift-F replaces the topmost diffraction pattern in the frontmost CrystalDiffract window with the latest pattern. By using the keyboard shortcut, one can quickly see the effect of a changed crystal structure.

   To accomodate these changes, the Calculate menu now has two diffraction submenus: one for powder diffraction, the other for single-crystal diffraction.

5. Interpolate Structures. You can now get CrystalMaker to interpolate between two selected structures in the Structures List, or between all structures in the Structures List.

   Interpolation is an invaluable tool when visualizing structural behaviour: it allows you to smooth the behaviour, resulting in a more professional-looking display. It also offers a seamless guide to the eye that makes it easier to follow "jerky" atomic motions - thereby reinforcing visual understanding of subtle structural behaviour.

   The Edit > Interpolate Structures command (also available from the Structure List's contextual menu) will prompt you to specify how many interpolations are required (i.e., the number of structures to be inserted between each pair of existing structures). CrystalMaker will then attempt to correlate each pair of structures, trying to match atoms with the same site occupancies, and then linearly-interpolating their properties (coordinates, displacement parameters, error values). If successful, new structures will be inserted into the Structures List, with appropriate titles.

6. Customizable Axes. The Axial vectors are now drawn at higher resolution and can be easily resized via new Length and Width slider controls in the Axes group of the Model Inspector. You can now also change the font name and size for axis labels.

   Axes can now be moved closer to the centre of the screen, via a new Inset slider control in the Position popover.

   A new Snug option is designed to allow larger, scaled axes, to fit more conveniently into the corner of the window. Instead of rotating about their origin, axes are rotated about their centre-of-gravity, so that they fit snugly into the window corner. This might be useful when preparing figures for publication.

   Axial labels can be toggled on or off, as can the cone-shaped "arrow heads". A new Axes rendering button, in the Reflectance group of the Rendering Inspector lets you change the reflectance properties - e.g., you can opt to have shiny axes, or give them a "flat", 2D style.

7. Customizable Atoms Inspector. The Actions menu in the Atoms Inspector lets you choose which columns should be displayed. New columns include:-

   • Label

   • xyz (fractional coordinates for crystals)

   • Multiplicity

   • Uiso

   Two column presets are available: Standard (which shows the current column layout) and Coordinates which shows a "flat" listing comprising: site Label, Occupancy, x y, z and multiplicity, m. Whilst most users will probably prefer the standard layout (which makes it easy to edit colours and styles), the Coordinates layout provides a scrollable listing of all atoms in a molecule, or all sites in a crystal.

8. Atomic Positions and Displacement Parameters are now shown in the Info Inspector. The lower, "Info" pane now sports two or three tabs, allowing direct access to the structure Overview, atomic Positions and - if present - Ellipsoids (i.e., atomic displacement parameters).

9. Spring-Loaded Sidebars. The Inspector, Structures List and Log can now be shown as slide-out panels, which pop back when the mouse is withdrawn. To show the panels, move the mouse towards the appropriate edge of the window; users with force-touch trackpads will feel a slight vibration ("haptic feedback") as the trigger point is reached. Shortly afterwards, the appropriate sidebar will slide into view, over and above any displayed structure. It will remain visible until the mouse moves outside the sidebar, whereupon the sidebar will slide back out of view.

   This is an excellent way of maximizing your screen space - especially in Full Screen mode - where any sidebars are by default hidden.

10. Saturation Control for Volumetric Data Slices. When visualizing volumetric data in the form of lattice plane slices, it is now possible to render out-of-range data values using the maximum or minimum colours of the current gradient. This is useful for highlighting a narrow range window, without the appearance of large "holes" in the slice.

    For example, one might want to set an intensity range between 40 and 60% with a red-white-blue gradient. Normally, data outside these values would be hidden, and only the lattice plane colour (if applicable) shown in the those regions. With the saturation option, data in the lower region (0-40%) would be shown in red and data in the upper region (60-100%) would be shown in blue - these being the extreme colours in the red-white-blue gradient.

11. Export Structures Command. When working with a multi-structure document, the individual structures can now be exported as separate documents in their own right, using the File > Export Structures command.

12. New Colour and Radii Synchronization Options. The Atoms Inspector Actions menu now lets you apply colours and atomic radii to all structures in a multi-structure document. The new commands are:-

    • Colour > Apply to All Structures

    • Colour > Apply Defaults to All Structures

    • Radii > Apply to All Structures

    • Radii > Apply Defaults to All Structures

    These commands will be useful if you wish to reset all structures to the default colour or radii values - or if you wish to use the currently-visible structure as a "template", and have its colours and radii applied to the remaining structures in the document.

13. Powerful New Video Options. When exporting Rotation or Animation movies, the export sheet now includes options to set the output scale and quality. Most users will find the default quality (the maximum afforded by the H.264 codec) to be satisfactory, but if smaller file sizes are required, the output quality can be reduced.

    We have undertaken extensive research on H.264 compression and have come up with our best approximation of a linear quality scale. A preview - an educated "guestimate" - of the output size is provided for guidance, but because of the way frame-to-frame comparisons are used in video compression, the final output size may be smaller.

    The option to output video at a smaller size will be useful to many users. It means you no longer have to resize your Graphics Pane to your desired output video size! Instead, you can specify your output size fraction in the video export sheet.

    The default video output quality has also been improved in this release. Firstly, a better choice of output colour space means that exported videos show brighter, more saturated colours. Secondly, users with "Retina" displays will experience higher-quality video.

14. Fat Sticks. Sometimes it is desirable to indicate structural channels using fat cylinders (passing between two dummy atoms). In earlier versions of the program, the maximum diameter of any bond or stick cylinder was limited by the diameter of the smallest ball-and-stick sphere in the structure. That generally precluded the display of "fat cylinders".

    In this version, we have removed this restriction for stick cylinder radii (as displayed in "Stick" or "Polyhedral" model types). That then allows very-fat cylinders to be shown.

    Fat Stick Example. A good example of this is provided by the new "Quartz Pole" structure, as found in the Examples collection in the Structures Library.

    Please note that for reasons of probity, ball-and-stick cylinder radii must not exceed the diameter of the smallest atom sphere.

15. PDB Crystal Export. Crystal structures can now be exported in the PDB file format, thereby preserving the lattice periodicity and any atomic displacement parameters. (Previously, crystals were saved as "molecules" in a PDB file.)

    Sadly, the PDB format remains very limited in its scope. For example, the format requires that space group characters should be in full international notation - but also limits the number of characters to 11, which is too few for some space groups. There is also no way to indicate different origin choices and, whilst one could convert atomic coordinates to the default origin choice, there is no way to shift the origin of the unit cell to the correct position. As a universal workaround, we export PDB crystal structures using the space group P 1.

16. Twinning. A new Transform > Unit Cell > Mirror Image command lets you generate a reflection of the lattice. If you have duplicated your structure, you can build up a model of a twinned crystal, with each structure copy being a mirror image.

    Twinning Example. A good example of the new Mirror Image command is provided by the "Polysynthetic Twins" example file in the Examples collection of the Structures Library.

17. Move Structures Precisely. When working with twin domains or domain boundaries, one might need to accurately and precisely reposition one structure relative to another. The Move tool now lets you constrain movement to the horizontal or vertical directions - if the shift key is held down. Note that as you move, the distance travelled is now displayed in real time. Alternatively, you can also use the Arrow keys to move the structure when the Move tool is active

    If you are using a force-touch trackpad (highly recommended, and standard with any new Mac), the Move tool provides haptic feedback to let you know when the structure is moved over the horizontal or vertical centre lines.

    Alternatively, the new Transform > Scale & Centre > Move Structures command lets you specify a precise distance in Ångstøm units.

18. Expanded Structures Library. This release includes 98 new reference structures, including 73 new minerals. We have also updated every calculated organic molecule, taking advantage of our new modelling engine.

    The minerals collection has been extensively updated and now boasts well over 400 phases! We have replaced old structures with better refinements, updated notes and added multiple views to existing documents. The "orthosilicates", "disilicates", "ring silicates" and "chain silicates" show the most changes; in particular, many new pyroxene and amphibole structures have been added, as well as two "biopyribole" phases. We have also added some lithium minerals and asbestos phases.

19. Improved Tool Strip Hiding. The Tool Strip now provides a more "stable" interface, remaining visible when the mouse moves from the Graphics Pane to another part of the window (e.g., the Inspector). The Tool Strip will vanish when the mouse exits the window. A new option allows the Tool Strip to be hidden after a period of inactivity, e.g., when giving a presentation in Full Screen mode, when the mouse has not been moved for a few seconds.

20. New default polyhedral style for anions. Earlier versions of the program let you assign a default polyhedral style for all sites (the factory setting was for a rendered polyhedron). Normally, this works well: if a structure has ions in 4-fold or higher coordination, rendered polyhedra can be plotted; ions with lower coordination states are plotted as spheres or left blank.

    The problem comes with very-densely-packed structures, such as orthosilicates, where oxygen ions are highly-coordinated; the program would then choose to plot both metal-centred polyhedra and oxygen-centred polyhedra, resulting in an inter-penetrating mess.

    Whilst some users might wish to display rendered-solid polyhedra around anions and cations, it is more usual to choose one set of ions as the polyhedral centres. For this reason, CrystalMaker's Preferences panel now has settings for anion and cation polyhedral styles. By default, we opt for rendered-solid cations and blank anions - but you can set your options to whichever works best for your needs.

    CrystalMaker recognizes the following elements as "anions": O, F, Cl, Br, I, At. All other elements will be regarded as "cations" in this context. However, you can always override the default settings by editing polyhedral styles in the Atoms Inspector.

21. Selectable Polyhedral Centroids. If a polyhedron is displayed in a translucent style, with the centroid atom visible, then this atom can be highlighted by rolling the mouse over it. The same atom can also be selected by clicking on it.

    Previously, whilst vertex atoms could be selected, any atom inside a polyhedron could not be selected, because its polyhedron "got in the way" and was highlighted instead. We now look inside the polyhedron to check whether a centroid atom is visible and, if it is, whether the mouse pointer lies directly above.

    Note that you can still select the entire polyhedron by clicking on it - just ensure that you click away from any vertex atoms or the centroid atom (if visible).

22. Program Reset Option. Holding down the command, option and shift keys at startup results in an alert asking whether you wish to revert to "Demo" mode. This is a useful way of resetting the program if, for some reason, your preferences have become corrupted.

    Note that if the system keeps trying to auto-open a corrupted text file when your launch CrystalMaker (which can make the program unresponsive) you don't need to reset the program. Instead, simply hold down the shift key at program startup, which stops the system from trying to auto-open any files.

23. Miscellaneous. This version includes numerous "under the hood" changes and the occasional bug fix, as detailed below.

    • "Hardened Runtime" is now enabled for this release. This latest Apple security feature reduces the chance of the application being attacked by viruses, malware or hackers.

    • Improved Distances Explorer. Changing the Search checkbox for one selected row applies the result to all other selected rows.

    • "Animation" and "Slideshow" presets have been added to the Play popover in the window toolbar. (This popover lets you control the animation speed and other options such as looping and auto rotation; to show the popover, click-and-hold the Play button until the popover appears.)

    • Improved loading of multiple files. A progress sheet is now shown for the complete file list.

    • The Add to Window panel now allows multiple selection.

    • A new Hide Sidebars in full-screen mode preference has been added to the Workspace pane of the Preferences panel. With this setting in effect, all sidebars - including the Ruler - vanish in Full-Screen mode (and reappear when exiting the mode). This is designed to reduce visual clutter and let you focus on your structure. (This feature works well with the new "spring-loaded sidebar" feature described above.)

    • The list of elements in the Elements pane in the Preferences panel can now be sorted by atomic number (Z).

    • Lighting previews, in the form of miniature stereographic projections, are shown in the Lighting group of the Rendering Inspector.

    • A new command has been added to select bonds between any selected atoms. This can be found on the Edit > Selection submenu and also on the Graphics Pane's contextual menu.

    • Commands to make text bigger or smaller can now be accessed from the Actions menu of the Info Inspector.

    • Orientation matrices entered in CMTX input files, are now verified to ensure they are consistent with the file's unit cell parameters.

    • Much faster text output. Our algorithm for generating unique site labels for atoms is now several orders of magnitude faster, resulting in quicker data export in "foreign" file formats such as CIF.

    • Faster import of CMTX files with thermal ellipsoid and/or site occupancy data.

    • Added a new green-pink gradient for use with volumetric data.

    • The Selection Inspector now shows the general equivalent position corresponding to the selected atom in a crystal.

    • The Info Inspector now shows the number of formula units ("Z") in the unit cell of a crystal.

    • New contextual menu for the Atoms Inspector. Most of the commands have been removed from the former menu - since these are available on the Actions menu and elsewhere. In their place are commands to Select Corresponding Atoms, Toggle Visibility and Toggle Atom Labels. These are properly contextual commands - they act on the clicked row, not necessarily on an existing selected row (unless the clicked row was also a selected row).

    • Users running macOS 10.10 "Yosemite" or 10.11 "El Capitan" will find that the Search Scope bar in the Library window is now hidden when not in use (later versions of the operating system automatically hid the scope bar - but the commands to do this are not available in earlier versions; however, we have been able to find a workaround in this version).

    • Deleting an atom or site in a crystal no longer resets the number of atoms drawn. Previously, the crystal was regenerated so that all atoms in the current plot range were made visible. That meant that any atoms which the user had explicitly hidden became visible again. Now, the program compares "before" and "after" states, to ensure consistency.

    • All text output now uses exclusively-ASCII characters, for greater reliability (previously the program used UTF8 encoding, but many programs do expect ASCII characters).

    • A crash when reading incorrectly-formatted - or mislabelled - binary files has now been averted. Please do not change "cmdf" file extensions to "cmdx" - the two formats are completely different and CrystalMaker needs to know which is which for successful reading.

    • An occasional issue with garbled volumetric data being rendered for XCrySDen (XSF) input files has now been resolved.

    • Fixed a bug with unit cell labels being incorrectly drawn when using a 3D Stereo plot with non-zero stereo standout.

    • SHELX files with "SFAC" cards that include atomic scattering factor data (rather than just element symbols) can now be read correctly.

    • An issue with ellipsoid styles for sites that lack thermal ellipsoids, has now been resolved.

    • The Centre on Bounding Box command now works correctly when multiple structures are visible.

    • Atoms Inspector tooltips are now correctly updated.

    • Exporting vector graphics with transparent backgrounds now works correctly.

    • Centrally-positioned axial vectors are now correctly exported in 2D graphics files.

    • Coordination numbers are now correctly updated when the structure is re-generated.

    • Selection using Lasso, Polygon or Rectangle now works correctly when perspective is enabled.

    • Stick polyhedral styles now show "elbow joint" atoms at the correct stick radii, rather than their original ball-and-stick radii.

    • The Log pane now has a minimum size, making it less likely that this pane will become squeezed out of existence on subsequent window resizing.

    • A rare problem with changing the symmetry in the crystal editor has now been addressed.

    • A very-rare bug with the Repair Fragments command has been fixed. This affected structures where atoms lay exactly on the plot range boundary and then became excluded when the structure was read back into the program.

    • Fixed a rare bug which could cause the colours of some atoms to be reset to black after editing their colours in the Atoms Inspector. This issue only occurred if the system colour picker were used to change a colour, followed by selecting text in the Notes pane of the Info Inspector.

    • Surfaces are now correctly updated if atom visibility is changed, or if sites are deleted. If a surface is already visible, then relaxing a structure will also update the surface display.

    • Fixed an issue plotting dotted-sphere bonds, which could show incorrectly-sized "elbow joints", or appear hidden when depth fading was enabled.

    • Resolved an issue with polyhedral labels being hidden or partially obscured when plotted on a "Retina" display.

    • Prevented a possible crash when trying to scroll the list of distances in the Distances Explorer.

1. Disordered Structure Support. This version supports SHELX "part" numbers and CIF "Disorder Groups". These indicate alternate versions of the structure and are displayed as separate structures in the Structures List.

   For example, a carbonate structure might have a CO₃ group (which is shaped like a helicopter rotor, with carbon in the centre and oxygens at the ends of the "rotor blades") in one of three possible orientations. Each orientation would have its atoms listed in the CIF file with their own _atom_site_disorder_group identification numbers, e.g., "1", "2" and "3" (or listed as separate "parts" in a SHELX file). Other, ordered, atoms in the structure would have their "disorder group" (or SHELX "part") as "0" (or left blank). Plotting the entire structure would show the three rotor orientations superimposed. However, at any instant in time, the correct structure would show just a single orientation: atoms from "group 0" plus one of the three possible orientations of the rotor, "group 1", "group 2" or "group 3". CrystalMaker would therefore show four structures in the Structures List:-

   • Composite structure (ordered atoms in disorder group 0, plus disordered representations, e.g., disorder groups 0 - 3)

   • Individual representation 1 (group 0 + group 1)

   • Individual representation 2 (group 0 + group 2)

   • Individual representation 3 (group 0 + group 3)

   By default, the composite structure is shown, but individual representations can easily be selected by clicking on their thumbnails.

2. Show Molecular Unit. An important new command has been added to the Transform > Atom Range and the toolbar's Tidy button. This combines the Show Asymmetric Unit command with the Repair Molecular Fragments command. This allows a quick view of an intact molecular unit, without the distraction of the full unit cell contents.

3. New Lighting Options with Multi-Touch Control. A fourth spotlight has been added, together with the option of backlighting. The latter allows for pleasing "halo" effects to be seen around sphere edges, when using rendered styles with specular reflection. Please see the new "Backlit Gold" example file in the Library.

   Each of the four lighting stereograms (in the Lighting group of the Rendering Inspector) now supports multi-touch. If the mouse pointer lies inside a stereogram, you can change the light direction using the following gestures: use "pinch" or "expand" gestures to change the elevation (i.e., to move the stereogram pole closer or further from the centre); use a rotate gesture to change the bearing.

   The design of the lighting stereogram has also been improved, showing a rendered background with buttons to toggle the stereonet or backlight.

4. Extended Error Propagation. Error values for bond distances are now displayed more prominently throughout the program, including in the Selection Inspector, various Log output commands - as well as the Distances & Angles file export.

5. Improved Synchronize Command. The algorithm for determining the centre of each structure has been improved, which should make it easier to match different structures in a sequence.

   A new Search Distance field allows the atom-level synchronization to be adjusted to cope with structures with large-scale atomic movements between successive frames.

6. Miscellaneous Changes. This version includes fixes for importing certain file formats, corrected gradient display options - and an expanded structures library.

   • A new command, Edit Bond Radii has been added to the Bond Inspector's Actions menu. This acts as a shortcut, opening the Model Inspector and showing the popover for the Bond Cylinder radius controls.

   • Atomic coordinates and bond distances are now displayed to greater precision in the Selection Inspector.

   • The maximum radius of "thin" bond cylinders has been increased from 60% to 75% of the regular cylinder radius.

   • Improved Show Molecular Cell algorithm. This now works for certain "edge case" structures (such as benzene) and provides a better display, focusing on molecules which are closest to the centre of the unit cell.

   • Major speed improvements for the Repair Molecular Fragments command - which is itself used in a number of other commands.

   • The "Auto Centre" menu command has been renamed as "Centre on Atoms" (to help distinguish it from the new "Centre on Bounding Box" command).

   • Constrained thermal ellipsoids are now loaded from SHELX files.

   • Exported CIF and CMTX files now enforce unique site labels.

   • Control-clicking in the Graphics pane now correctly shows a contextual menu.

   • Moving the Arrow tool over an atom vector now correctly highlights the vector magnitude and orientation.

   • Fixed an issue with massive thermal ellipsoids being shown for sites without any thermal ellipsoid data.

   • The Distance Explorer no longer shows a Save File prompt when attempting to close its window.

   • The Centre on Bounding Box command now takes the unit cell frame into account.

1. Optimize Colours for Red/Blue Stereo. When using red/blue stereo, it is important to ensure that colours are compatible - in particular, red and cyan hues should be avoided, as these will be cut out by the coloured spectacle lenses. To make things easier, the new Optimize for Red/Blue Stereo command automatically shifts all colour hues away from the red/cyan "danger zones". This new command is available via the Atoms Inspector: either from the contextual menu, or the Actions menu popup (the cog icon in the top right-hand corner). The command can be found on the Colours submenu.

2. Miscellaneous Changes. This version includes fixes for importing certain file formats, corrected gradient display options - and an expanded structures library.

   • Fixed text file import for certain file formats. Changes to our text processing engine caused the program to hang up when processing certain (but not all) file types. This issue has now been resolved.

   • The Colour/Gradient colour buttons in the Background group of the Rendering Inspector now show the correct tool tips.

   • This version includes new mineral phases as well as additional synthetic materials corresponding to colour pigments, e.g., "Primrose Yellow", "Cobalt Blue", "Han Blue", "Chrome Green" and "Viridian".

1. Comprehensive Preferences. Major improvements have been made to the Preferences panel, which now provides access to virtually every possible setting that can be made.

   The Atoms, Bonds and Polyhedra panes have been combined into a single Model pane. This uses a tabbed interface to allow individual settings for Atom Spheres, Ellipsoids, Bonds or Polyhedra.

   The Model Extras pane also now has a tabbed interface, making it much easier to navigate - and providing room for more settings.

   A new Rendering tab gives full control over the background, reflectance, and depth settings.

2. Video Tutorials. A new Help > Video Tutorials command provides quick access to an extensive series of new audio-visual tutorials: comprising nearly two hours of training.

3. Change Atom Type with Add Atom Tool. You can now change the element type of an existing atom whilst using the Add Atom tool. Click on an atom to highlight it, choose a new element type from the Atom Picker palette, then click on the atom for a second time to change its type.

4. New Auto Centre Option. The Transform > Scale & Centre submenu includes a new auto-centring option, Auto Centre Bounding Box. Unlike the conventional Auto Centre command, which moves the centroid of the structure to the screen centre, the new command considers only the outer bounds of the structure - its virtual "bounding box", and positions this centrally. The differences between the two commands will be most evident for asymmetric models - e.g., a triangular molecule.

5. Miscellaneous Changes. This version includes a plethora of additional, "under the hood" changes and enhancements.

   • Improved Elements Preferences with a larger and clearer periodic table of the elements, and the addition of a pair of left/right buttons to permit easy browsing of the preset tables.

   • Improved algorithm for detecting inter-connected structures. This algorithm helps prevent problems when trying to use commands designed for molecular crystals. The old algorithm tested for fully-interconnected 3D frameworks, but not 1D (chains) or 2D (sheet) structures.

   • Streamlined Packing and Distance Explorers: the Inspector panels have been made narrower and their control layouts neatened.

   • The Calculate > Cavities command is now correctly disabled for a molecule.

   • Fixed a potential problem importing volumetric data from an XSF file.

   • Fixed an issue with the automatic detection of unconventional Monoclinic space groups. In certain cases, a conventional setting was mistakenly being applied (e.g., P 1 2₁ 1 instead of P 1 1 2₁).

1. Cavity Finder. A new Calculate > Cavities command lets you detect large voids within an arbitrary structure - with the option of visualizing their positions and sizes directly on the screen.

   A sheet window lets you specify the minimum void size (hint: the default size of 2 Å works well for most structures); the program then analyses the structure, locating empty regions large enough to position an atom of the required size - and proceeds to calculate the maximum atomic radius that can fit into the structure at these positions. Results are printed in the window log.

   If you choose the visualization option, then new, dummy sites are created at the void locations. These are displayed as translucent spheres, whose radii match the sizes of the surrounding voids.

   Please note that this algorithm uses any existing radii in the structure; the program does not apply Van der Waals radii (although you could manually reset your radii to these values, if required).

2. Faster Surfaces. A new algorithm makes surface display considerably faster than before - particularly for massive structures. Because of the new (voxel-based) algorithm, some of the old surface options (e.g., colour-by-atom and mesh display) are no longer available.

3. Smoother Volumetric Data. Sparse volumetric datasets now use bicubic interpolation to reduce noise and improve clarity. Varying degrees of "oversampling" are used, depending on the number of input data points.

   When adjusting iso-surfaces or iso-volume thresholds using the Range popover, you now have the option of temporarily turning off the oversampling and using a "Fast Redraw" mode; this makes it easier to make finer-scale adjustments. Normal, high-quality drawing resumes at idle time.

4. Surface Map. A new "Surface Map" option is available, letting you visualize Space-Filling, Van der Waals, or Solvent-Excluded surfaces. Unlike the regular surface overlay, this is not a "real time" surface, but a "one off" calculation, allowing more control and greater flexibility.

   Whereas the surface overlay applies to all visible atoms - and is updated as atomic visibility changes - a "Surface Map" is created once, and will persist even as the number of atoms changes. This allows you to control which atoms have a surface around them. You can also control the quality (number of "voxels") and detail in your surface.

   Surface Maps can be created either using the Calculate > Volumetric Data > Surface Map command, or by using the Add Volumetric Data submenu on the Volumetric Data actions menu.

   Whilst Surface Maps are designed for periodic, crystal structures, you can opt to make your surface map aperiodic, by turning off the Periodic checkbox in the Surface Map sheet.

5. Distance Map. A new "Distance Map" option makes it easier to visualize cavities and channels in complex crystal structures. For each unfilled point in space, the distance to the surface of the closest atom is saved. You can then customize the range of distances to be shown, e.g., to visualize all areas that an ion of a particular size can access.

   Distance Maps can be created either using the Calculate > Volumetric Data submenu, or by using the Add Volumetric Data submenu on the Volumetric Data actions menu.

6. Powerful New Vibrations Explorer. The Vibrations Explorer now includes significantly-enhanced functionality, accessed via a dedicated Inspector pane (rather than occasional popover controls). Users can immediately adjust the animation parameters and opt to display the intensities of IR modes directly in the Modes list (shortcut: click the Modes list header to toggle between single- or double-column display - the latter with IR intensities shown).

   The IR spectrum can now be shown as a function of transmittance as well as absorbance, and the x-axis can be displayed in ascending or descending order (the latter option may be more familiar to chemists). You can now choose a peak-shape function, customize the peak width, add a shadow, change the line width or its colour.

7. Ring Calculations. A new Calculate > Rings Through Atom command prints detailed information for rings, up to a default limit.

8. XSF File Import. CrystalMaker can now import structure files generated by the old X-Windows "XCrySDen" program. CrystalMaker can read molecule, crystal and animated (AXSF) files. In the latter case, a sequence of structures is read from the file and added to the Structures List, ready for instance animation via CrystalMaker's Play command.

9. Rotate Quick Links. A new Rotate submenu has been added to the Transform menu. This includes commands to rotate Left, Right, Up and Down as well as Clockwise and Anti-Clockwise. Keyboard shortcuts are available, allowing for quick control over the orientation. The rotation steps are the same as in the Rotate popover (default values are 90°).

10. Open Structure in New Window. You can now select a structure and create a copy in a new window, using the File > New Window with Structure command, or via the Structure List's New Window with Selection contextual menu command.

11. Improved Ellipsoid Workflow. We have streamlined the way in which the "plot ellipsoid as sphere" option works. Previously in version X, one would click the Plot Ball-and-Stick Sphere button in the Ellipsoid style popover, and CrystalMaker would display the ellipsoid in the specified site's atom style. This worked well for some users, but changing the atom style required a round trip to the Ball-and-Stick model type, which other users found confusing.

    In this latest version, all thermal ellipsoid styles are set from the same popover, and the "plot as sphere" option is now a checkbox.

12. Improved Memory Performance. Closing a window or removing a structure from an existing window now allows the operating system to reclaim the memory correctly.

13. Miscellaneous Changes. This version includes better performance and miscellaneous bug fixes.

    • New Reapply Bond Specifications command, added to the Bond Inspector's Actions and contextual menus. This lets you regenerate bonding for all specifications in the current structure.

    • Easier volumetric dataset creation: double-clicking on an empty row in the Volumetric Data table now displays a popup menu letting you choose what type of dataset to create.

    • Double-clicking on the minimum or maximum fields in the Bonds Inspector now edits their values.

    • Added new shortcuts to the Crystal and Molecule editors: double-clicking on an empty row now creates a new row (i.e., has the same effect as clicking the "+" button).

    • Faster graphics: OpenGL 4.1 performance is now correctly enabled (where permitted) at startup, resulting in faster display. However, for maximum compatibility, OpenGL 3.2 is now the preferred default.

    • Easier editing of structure list titles: the title of a selected structure can be edited by pressing the Enter key.

    • Concave polyhedra now have their concave "inner" faces drawn, unless "curvature shading" is enabled. This brings the Mac version into line with the Windows version.

    • Translucent atom, bond and polyhedral previews are now displayed correctly when using OpenGL 3.2 graphics.

    • The mouse pointer is now correctly reset to the arrow pointer when inside a popover.

    • The Rotate popover can now be moved when it is over the Graphics pane.

    • Faster display of polyhedra with thick edges; a (rare) problem with edges becoming extended outside the structure has also been resolved.

    • Improved ring selection algorithm.

    • Compact volumetric datasets. Porosity and surface datasets are now saved in a more efficient manner, resulting in considerable reduced file sizes (60-70% smaller).

    • Faster rotation for massive crystal structures.

    • The Add Molecular Centroids command now uses zero occupancy for its new, dummy sites - thereby leaving the structural formula unchanged.

    • Atom labels now work correctly for "Stick", "Wireframe" and "Thermal Ellipsoid" model types.

    • Improved SHELX import. Site labels saved in the SHELX files are now respected; thermal ellipsoids loaded from the file can now be displayed on screen.

    • Fixed occasional glitches with multi-structure animations. Atoms without bonds, or off-centred structures could appear. These were related to a performance optimization in the previous version of the software and have now been resolved.

    • Displaying "noisy" volumetric data should no longer cause a crash.

    • The Radii submenu of the Atoms Inspector Actions menu is now correctly populated at program startup.

    • Volumetric data selection now only applies for visible datasets.

    • Fixed a potential bug with the lattice planes Move to Intercepts command.

    • Orientation matrices ("OMAT" cards) are now correctly read from CrystalMaker (CMTX) text files.

    • Pressing the Reset Matrix button in the Cell Transformation sheet now clears any previously displayed error messages.

    • Fixed a potential bug with the Add/Delete Bonds tool: it had been possible to self-bond an atom, which could cause problems during subsequent operations!

    • Improved CIF import: importing thermal ellipsoids saved in the (very rare!) B_ij format now works correctly.

    • Improved removal of duplicate atoms for hexagonal or trigonal structure.

    • Exporting ultra-high-resolution graphics (dimensions greater than about 16,000 pixels) now works correctly.

1. Faster Rotation & Scaling. This version offers a significant performance improvement for rotation and scaling operations. In our tests, for complex structures, rendering was 66% faster than before, thanks to optimizations in the way graphics objects are copied to the video card.

2. D-Spacing Calculator. We have a added a new calculator palette which displays the d-spacing for a specified lattice plane (hkl indices) for the frontmost document window - and with the option to print the result in the window log. To access the calculator, choose: Calculate > D-Spacing Calculator.

3. Isolate Fragment. A new "Isolate" command has been added to the Graphics Pane contextual menu (and to the main Transform > Selection sub-menu). The Isolate > Fragment command combines two previously-separate steps:

   Expand Selection > Fragment

   and:

   Isolate Selection.

   The three Isolate commands have been moved to a submenu on the Graphics Pane contextual menu. They are: (Isolate > Selection; Isolate > Fragment; Isolate > Molecule).

   As a quick reminder: "Fragment" refers to visibly-interconnected atoms, whereas "Molecule" refers to ALL interconnected atoms, regardless of their visibility.

4. Improved Porosity-Map Generation. Earlier versions of the program used a single, default "voxel" size for all structures. Whilst this was designed to work well for typical inorganic structures, extended structures - such as Molecular-Organic Frameworks (MOFs) - have such massive unit cells that using the default value would require excessive amounts of (precious) system RAM - over 50 GB for some structures.

   This version now computes a sensible voxel size, based on the current plot dimensions (and the same algorithm has been extended to the Electron Density Map). Users can still override this value, using the sheet controls provided.

5. Expanded Structures Library. CrystalMaker now includes all known crystal structures for the elements (at ambient conditions), plus a number of additional phases formed at other temperatures and pressures. Many other structures have also been added - including a new "Pigments" thematic library.

6. Miscellaneous Changes. This version includes improvements to nearest-neighbour and ring selection, CIF import - plus a number of bug fixes.

   • Improved nearest-neighbour selection: the program now skips any hidden atoms (i.e., this behaves akin to the "Fragment" rather than the "Molecule" commands).

   • Print to Log buttons in the Angle- and D-Spacing Calculators now display the window log if it isn't current visible.

   • CIF files with inconsistent site labelling between multiple "loop" statements are now handled more gracefully.

   • The Duplicate Selection command now accepts negative offsets.

   • In the rare event that a user enters a blank minimum or maximum bond distance in the Bonds Inspector, CrystalMaker now intervenes to inject a sensible value, thereby avoiding a potential crash.

   • More refinements to the Ring Selection algorithm mean that rings with side chains attached can now be reliably selected.

   • When moving one or more atoms in a crystal, all coordinates are updated in real time, meaning that data export uses fully up-to-date data.

   • Fixed a (very-rare) issue with the coordinate system becoming inverted if the scale was reduced to zero. This could happen with a very-rapid multi-touch "pinch" gesture on a trackpad.

   • Fixed a bug with the Merge Atoms command which could cause atoms in neighbouring unit cells to be made visible.

1. Smaller File Size, Reduced Memory Requirement. The "Quick Tour" videos have now been replaced with a direct link to our website "Video Tour". This makes the application much smaller (disc image is 25% smaller) and means that we can add more videos without worrying about size issues.

   The Library Browser now defers preview generation until drawing time, which greatly reduces the program's memory footprint during normal use.

2. Expanded Structures Library. A large number of new crystal structures have been added in this release, including the crystal structures of most of the elements. These can be found in both the Reference Library and also in a dedicated "Crystalline Elements" teaching library.

3. Miscellaneous Changes. This version includes improvements to atom label outlines, ring selection, plus a number of bug fixes.

   • Improved atom labels. The outlines are now slightly rounded, which avoids spurious ascenders or descenders. The outline width now scales with the font size.

   • Faster assignment of unique site labels (using the Atoms Inspector).

   • Electron density maps now choose the default lattice plane slice (if no lattice planes are currently visible) more accurately, choosing a plane that is approximately perpendicular to the view direction.

   • Improved Ring Selection algorithm: this can now cope with rings containing odd numbers of atoms.

   • The Angle Calculator now works correctly for non-orthogonal axes.

   • Legacy "CMMF" molecule files converted from crystals with thermal ellipsoid data, can now be read into CrystalMaker X.

1. Powerful New Volumetric Data Display. Major improvements have been made to all aspects of volumetric data display and manipulation, including true iso-surfaces, iso-lines, new colouring options, smoother display, inline list controls, histogram previews, a real-time range slider with colourisation, mode-, median- and mid-range display presets and the ability to define range thresholds in raw units.

   • CrystalMaker now supports the display of true iso-surfaces (in addition to the existing iso-volumes). You can use the new range controls to specify equal minimum and maximum thresholds, or use the new "Median" and "Mode" presets and then drag the range slider to watch the iso-surface vary with value.

   • The Volumetric Datasets list includes an Info button which displays a summary of the dataset in a popover. Information includes dimensions, voxel size and volume, minimum and maximum values, the mean, median and mode.

   • Another inline list control is a Range button. This provides a summary of the current range limits (expressed as fractions of the overall data range). When clicked, a new Range popover appears. This previews the data range and its values, in the form of a histogram, with a real-time, coloured, range slider. A new "Remap Colour Range" checkbox lets you squeeze the current colour gradient into the min/max interval, or have it stretched between the absolute data range. (The coloured range slider makes this feature very intuitive.)

   • Data thresholds can now be specified using raw (input) data values, in addition to relative (percentage) values.

   • Data thresholds can be interactively scanned by locking the minimum-to-maximum interval (padlock icon in the Range popover) and dragging the range slider or using the min/max stepper controls.

   • You can now browse between different volumetric datasets in the same window by option-clicking their visibility checkboxes. This will automatically make the clicked dataset visible and hide any remaining datasets. (Of course, you can still have multiple datasets visible simultaneously, if you wish.)

   • Three separate colours can be used for iso-volumes: the "inside" and "outside" colours, as well as the truncation colour (e.g., where the data are cut by the unit cell or selection range). Note that, for iso-surfaces, the truncation colour is never shown (the surface is infinitely thin).

   • Iso-surfaces and iso-volumes now appear much smoother with less spurious "noise".

   • Translucent lattice plane sections are now possible: letting you see through lattice plane slices and give a greater sense of depth.

   • Volumetric data visualized as lattice plane slices can also be seen as "isolines" when a single threshold value is specified.

2. Streamlined Inspector. The Inspector has a clean new look, with a strong tabbed design, more compact control groups, and the addition of a new Volume Inspector.

   • Navigation between the various inspectors now uses tabs, rather than highlighted icons. This should prove clearer for many users - and strengthens the correspondence between an inspector's controls and its tab.

   • The Atoms, Bonds, Lattice Planes and Volumetric Data lists now have Actions buttons with drop-down menus. These provide immediate access to key functions (which were previously buried within contextual menus).

   • A new shortcut has been provided for adding a new Bond Specification or a new Lattice Plane. Simply double click on a blank row in the respective list to add a new entry.

   • A new "Volume Inspector" has been added for display of volumetric data and lattice planes (whose lists have been moved from the Model Inspector). This helps to declutter the Model Inspector, whilst providing a more focused interface for the Lattice Planes and Volumetric Data lists. Including both lists in the same inspector makes it easier to manage volumetric data visualized as lattice plane sections.

   • The Model and Rendering inspectors are now more compact, using popovers to display non-critical controls. By default, more of the control groups are shown opened for new structures.

   • The Unit Cell group in the Model Inspector is now hidden if the current structure is not a crystal.

   • Panel-wide contextual menus are available for both Model and Rendering inspectors. These allow you to quickly save or reset multiple settings, as well as expand or contract all control groups. To display the panel-wide contextual menu either: right-click below the bottom of the list, or right-click on the Inspector icon.

3. Pie-Chart and Fuzzy Spheres. Four new sphere styles have been added to the program, comprising 2D and 3D variants of "Pie Chart" spheres and "Fuzzy" spheres.

   Pie-Chart spheres provide a visual indication of mixed (or missing) site occupancy. The colours of the various elements are used to colour different sectors of the sphere; any missing components are indicated by a translucent sector. Note that element colours are chosen from the active element table; colours may differ from system to system.

   Fuzzy spheres vary in transparency from the centre to the edge, creating a better illusion of a filled atom, whose thickness varies from centre to edge.

4. Library Formula Search with Scope Bar. When performing a search in the Library Browser, a new Scope Bar appears, making it easier for you to define your search criteria. By default, the search location is the (new) Reference Library (which replaces the former "All Structures" folder) - since this is designed as the central repository for reference structures.

   • Search Location buttons let you reset the search location to your currently-navigated folder, your Favourites, or All folders.

   • You can now opt to search for just crystal structures, molecules, or both. Note that if a document contains both crystals and molecules, it will show up in all searches.

   • CrystalMaker now lets you choose what kind of content to be searched:-

     • By filename.

     • By notes.

     • Formula contains elements (e.g., "Si" brings up Si, SiO₂ and Al₂SiO₅)

     • Formula matches elements (e.g., "Si" only yields Si)

     • Exact formula match.

     The "Exact Formula Match" is a new option. For the case of crystals, element proportions are matched (e.g., "Si2O4" will be treated as "SiO2"). You no longer have to type spaces between element symbols - but if you do omit spaces, you will need to use the correct capitalization e.g., "Al2O3", not "al2o3".

5. Expanded, Reorganised Structures Library. This version includes a large increase in the number - and quality - of crystal structures. The organisation of the library has also been changed, so that it is easier to navigate and search. Highlights include:-

   • Reference library with 400+ crystal structures of minerals, ~300 other (non-mineral) inorganics and hybrid materials and ~300 organics (crystals and molecules)

   • New Crystal Structures of the Elements Teaching Library

   • Expanded "Structural Architecture" library (Teaching Library) with detailed animations of the crystal structures for: calcite, feldspar, quartz, spinel, YBCO supercondutor, zeolite ZK5.

   Many formerly-separate files have been consolidated into multi-structure documents, e.g., phase transitions in quartz, cristobalite and leucite; structural views (cages, chains), etc. For this reason, the Library Browser now displays both the total number of documents and the total number of structures (if different).

6. Haptic Feedback. You can now feel the structure you are measuring! If your trackpad has haptic feedback enabled (System Preferences > Trackpad > Force Click and haptic feedback) then the screen tools provide feedback as you move around your structure. For example, you will feel a subtle click as the Arrow tool passes over an atom, or a bond angle is displayed.

7. Live Bond Angle and Distance Rollovers. The Bond Angle tool now provides a live feedback of bond angles as you move the mouse around your structure - no clicking is required! Similarly, the bond distance tool lets you measure distances without clicking.

8. Powerful Polyhedral Face Generation. You can now customize how you would like your polyhedral faces to appear by changing the out-of-plane tolerance for vertex atoms. This lets you display larger faces with more vertices.

   A summary of the number of faces with different numbers of vertices is now displayed in the Selection Inspector - and can be printed to the window log. CrystalMaker uses the standard convention [A^xB^yC^z] to indicate the presence of x faces with "A" vertices each, y faces with "B" vertices and z faces with "C" vertices.

9. Variable-Translucency Atom Spheres. You can now specify the amount of translucency to be used for any Atom spheres with the translucent style. Use the slider control in the General group of the Model Inspector.

10. Enhanced VASP File Import. CrystalMaker X can now import dual datasets from CHGCAR and other VASP files. VASP files without file extensions can be dragged-and-dropped into the Volumetric Data list - as long as these files have recognised filenames: CHG, CHGCAR or ELFCAR.

11. Expanded User's Guide and Tutorials. The CrystalMaker User's Guide is now 360 pages in length and has had its layout and content improved. Two new chapters - covering Labelling & Annotation and Rendering make it easier to find key concepts. New content has been added to illustrate some of the new features introduced in version 10.2, as well as to improve the general coverage.

12. Miscellaneous Changes. This version includes a plethora of additional, "under the hood" changes and enhancements.

    • Most of the Quick Tour videos (Help > Quick Tour) have been updated for this release.

    • New menu items to show or hide atom labels have been added to the Model menu.

    • 3ED volumetric data files can now be imported.

    • Volumetric Dataset Resampling: datasets with different numbers of points can now be combined via addition or subtraction. CrystalMaker upsamples datasets to ensure they can be merged.

    • Screen tools now work in stereo-pair mode. You can also make measurements or selections on either side of the screen.

    • Hidden lattice planes are now shown with disabled controls in the lattice planes list.

    • Thickness of lattice plane edges (e.g., where a plane is truncated by the unit cell range) can now be set in the General group of the Model Inspector.

    • Improved Rotation Movie export: now allows choice of rotation axis and will honour a custom axis set in the Spin control.

    • Improved Distance tool display, makes it easier to measure smaller distances.

    • VASP files containing element symbols on line 6 can now be successfully imported.

    • COLLADA 3D files now use higher-quality thermal ellipsoids.

    • (Non-Standard) Guassian CUBE files which do not contain line breaks after each group of xy data can now be loaded. In addition, structures with non-orthogonal axes now have their cell vectors correctly calculated.

    • Fixed an intermittent bug with parallel sets of lattice planes.

    • Fixed a problem trying to move multiply-selected lattice planes to their intercepts.

    • Fixed a problem with applying settings by clicking - rather than tabbing - in control fields. This affected various sheets, including the View Direction, Add Centroid, Scale, and a number of other controls.

    • Fixed a problem with the Cluster popover, which made it difficult to change the centre via the combo box.

    • Automatic window restoration (e.g., re-loading a text or legacy document following a crash) now works correctly, with files loaded instead of empty windows.

1. New Atom Labelling Options. We have added four new labelling options for crystals, including x, y or z fractional coordinate displays, plus a fractional height option.

   The fractional height is the height of atoms relative to the unit cell repeat distance normal to the screen. The heights will actually be expressed relative to the closest lattice vector (with indices in the range -1 to +1) to the screen vector.

   For clarity, CrystalMaker finds the closest lattice vector in one of the sets <100>, <110> and <111>, and uses this to compute the fractional height. This method avoids massive changes in the fractional height as the unit cell is tilted slightly, e.g., if the view direction changes from [001] to [1 1 999]!

   For example, if the crystal is viewed approximately down the [001] direction, heights will be fractions of the 'c' parameter, whereas if the crystal is viewed approximately down [110] then heights will be fractions of the vector a + b.

   This option works best when the structure is being shown in projection down a major symmetry direction. Note that, for extra clarity, fraction characters are used in preference to decimals, wherever possible.

2. Streamlined Reflectance Group in the Rendering Inspector. The individual slider controls and presets have been moved into popover controls for each model element (spheres, bonds, polyhedra, etc.) and are accessed via named buttons. This helps declutter the interface and reduces the amount of vertical space required. The default layout now has the first three Rendering panes open.

3. Streamlined Lattice Planes Group in the Model Inspector. The lattice plane position controls (slider and preset buttons) have been moved to popovers, which are accessed via new Move buttons in the Lattice Planes list.

   This change is part of our longer-term plan to move both the Lattice Planes group and the Volumetric Datasets group to separate inspectors, thereby reducing the size of the Model Inspector and making it possible to display open groups for easier access.

4. Rationalised Menus. More commands have been added to the main menu bar, thereby making it easier to access commands which were previously buried in contextual menus. For example, a new View Direction submenu in the Transform menu provides access to the View Lattice Plane Horizontally command (from the Model Inspector); other commands added include the Slice Crystal, Make Slab and Insert Space commands.

   The Transform > Molecular Crystal submenu has been eliminated; its commands have been moved to the Atom Range submenu or the Model menu.

5. Deluxe User's Guide. The CrystalMaker User's Guide now has a new Gallery chapter with illustrated structures - many of them newly commissioned for this version - and descriptions of how they were generated. We have also expanded other sections, including a topic on disorder, plus more detail about the multi-structure capabilities of the software.

6. Expanded Structures Library. New phases include VO₂ and phases in the Co - Pt system. A new "Building YBCO" teaching document has been added to the "Structural Architecture" section, and the various phases of ice have been updated for this version.

7. Miscellaneous Changes. This version includes numerous performance and interface enhancements plus bug fixes.

   • Added tool tips to the document window's Rotate popover.

   • Improved Cluster popover: values can now be entered without distance units; replotting only occurs if values are changed.

   • Any surface display is now hidden in the Vibrations Explorer - as keeping the surface visible would require multiple recalculations (for each frame of the sequence), which would slow down the animation.

   • Added syntax checking when editing element symbols in the Atoms Inspector.

   • The Depth Fading group in the Rendering Inspector has been made shorter by reducing the height of the depth graph.

   • Added a contextual menu to the Lattice Planes list.

   • Moved the Convert Labels to Textboxes command from the Transform > Selection submenu to the Model menu.

   • Lattice plane intercepts are now recalculated when the plot range changes.

   • Fixed miscellaneous graphics glitches - chiefly involving Intel Integrated Graphics (as supplied on MacBook, MacBook Air and 13" MacBook Pro computers). We have been forced to workaround what appear to be bugs in the current drivers. Symptoms included missing previews, random atom label display and missing bond previews. Note that we now force the use of "compatibility mode" for all computers with integrated graphics; this should ensure more-reliable operation.

   • Exporting an STL file no longer adds hidden volumetric datasets.

   • Fixed a rounding error when changing the plot range using the little arrow controls - which could cause some atoms to remain hidden, even though the displayed range appeared to suggest that they should be visible.

   • Origin offsets in CUBE files are now respected.

   • Secondary bonds are now correctly calculated for atoms with no primary bonds.

1. Full User's Guide. The CrystalMaker X User's Guide is now complete! This edition contains 310 pages with a preface, 11 chapters, 4 appendices and a glossary. It is the definitive guide to using the program and is fully illustrated throughout.

   The CrystalMaker Tutorials document has also been extensively revised for this version, with improved layout, reorganised sections and a more-focused workflow. The two tutorials provide a quick and easy introduction to using the software. Users upgrading from an version 9 or earlier are strongly encouraged to invest a few minutes of their time in completing at least Tutorial 1: The Basics, as this will help explain the basic interface design and hidden features.

2. Rationalised Menus. Many menus which were only available via contextual or the Selection Inspector's Actions menus, are now also available on the main menu bar. Examples include:

   • Edit menu: Merge Structures (which is similar to the more-primitive Place Molecule command in earlier versions of the program)

   • Transform menu: Renamed the Axial Range Limits command to Set Range (as used in all previous versions of the program). Added Hide Selection, Isolate Selection, Isolate Selected Molecule commands to the Atom Range submenu. (These commands were previously only available via the Graphics Pane's contextual menu.)

   • Calculate menu: Added new Atom Info, Bonding Info and Angle Info commands. Moved the List Atoms and related commands to a new Structure Report submenu.

   Some commands have been renamed to make them easier to understand, e.g., File > Take Snapshot becomes Edit > Duplicate Structure.

3. Output Graphics Resolution. A new Output Resolution setting is now available in the Graphics pane of the Preferences panel. This lets you specify the resolution to be used when copying a graphic to the clipboard, exporting it to disc, or printing. The resolution is now also directly applied to the output file (although not all graphics programs will respect this setting).

   Example 1: if your screen image were 10 inches wide at a screen resolution of 72 dpi, then an output resolution of 144 dpi would result in an output image 10 inches wide with a resolution of 144 dpi.

   Note that, when exporting an image to a graphics file, you can make the image larger - i.e., increase the number of pixels - by applying a magnification; this does not change the actual resolution of the output image.

   Example 2: exporting your 10-inch screen image to a 144 dpi graphics file using a magnification of 2, would result in an output image 20 inches wide with a resolution of 144 dpi.

4. Improved Label Positioning: Improved label metrics allow more precise (and consistent) positionning of atom and bond labels. Bond labels are now centred over the visible portion of the bond cylinder, rather than at the midpoint between the two atom centres; this gives better results when the two atoms are of differing sizes.

5. Convert Labels to Textboxes. A new command to convert any selected atom labels to new annotation objects has been added to the Transform > Selection submenu. This command replaces the existing atom label with a new textbox - which can be repositioned with the Arrow tool. (Note that, as with all annotation objects, the textboxes exist in an overlay, and do not rotate when the structure is rotated; these are designed for final-stage preparation of diagrams or journal figures.)

6. Self-Rotating Animations. A new Auto Rotate checkbox has been added to the Play popover. This lets you start an animation with auto-rotation ("spin") enabled.

   Both animations and auto-rotation now also reset the structure(s) to the original orientation at the end of their activity.

7. New Range Commands. Two new commands have been added to the Transform > Atom Range submenu, to make it easier to quickly work with a selection, and to tidy up massive structures.

   • The Trim to Selection command will reset the current plot range to a box that neatly spans the range of selected atoms. This is useful for tidying up the display, particularly if one is working with a massive structure.

     Note that whilst one can easily isolate a group of atoms, by effectively hiding the rest of the plot range, this still leaves (potentially) a large number of atoms in range. Those in-range atoms could slow down the program and increase file size.

   • The Hide Minimally-Bonded Atoms command hides all atoms with fewer than two bonds (e.g., H and any cavity or channel ions). This may be helpful when working with massive, complex frameworks such as zeolites or MOFs.

8. Improved Toolbar Delay Buttons. Refined the behaviour of toolbar buttons with combined actions and popovers - e.g., Spin and Play. Previously, clicking-and-holding such buttons would eventually display the appropriate popover - but would also start the action. Now, a single click triggers the button action whereas a prolonged click-and-hold only displays the popover. This makes it easier to customize actions without actually executing them.

9. Structural Architecture Library. This new library is part of the Reference Library > Teaching Collection in the Library Browser. It includes animations illustrating three common minerals (which are important prototype structures for synthetic analogues):

   • Building Feldspar (NEW!)

   • Building Quartz

   • Building Spinel

10. Miscellaneous Changes. This version includes numerous performance and interface enhancements plus bug fixes.

    • Added a keyboard shortcut, cmd-G, for the File > Export Graphics > 2D Graphics command.

    • Added 15 unconventional monoclinic F space groups.

    • Improved Duplicate Structure command. The new structure now appears selected (visible) and directly beneath the source structure in the Structures List.

    • Added a new File > Duplicate command, which opens a new document window with a copy of the former document (but does not save the file to disc). Note that this is subtly different form the File > Save As command, which re-saves the current document to a new location on disc.

    • Library files can now be reverted using the File > Revert to Saved command. This allows you to return the displayed structure to its original, saved state. Note that you cannot overwrite library files, but you can save a copy using the File > Save As command (hold down the option key to enable this) or the new File > Duplicate command.

    • Improved the Vibrations Explorer so that when switching between different vibrational modes, the current orientation and scale is now retained.

    • Online Help now uses larger text and works better on Windows high-DPI displays such as the Microsoft Surface Pro.

    • The graphics window can no longer be resized whilst the Export Graphics sheet is open. This is to prevent confusion when specifying the output size/magnification - which is based on the current window.

    • Added Help commands to the Rendering-, Model- and Selection Inspectors' contextual menus. These links bring up the appropriate help pages, referring to the specific Inspector being displayed.

    • Textboxes can now be edited even if the Selection Inspector is hidden.

    • Improved layout in the Bond & Sphere options group of the Model Inspector.

    • Improved Rotator popover design, featuring a circular background image. The popup angle menus - as used in the Vibration-, Packing- and Symmetry Explorer windows - now functions correctly.

    • Fixed an issue which could cause the display to freeze if multiple structures with unit cells were left auto-rotating and/or animating for a prolonged time period.

    • Fixed an occasional issue with the display flashing (structure being hidden and then reappearing) after a fast animation.

    • Addressed an issue with certain dual-origin orthorhombic space groups which could cause the origin setting to be reset to 1 when the structure is edited.

    • Fixed a glitch which could cause row selection in the Selection Inspector to be hidden.

    • Fixed an issue (introduced in the previous version) with automatic bond generation not correctly refreshing bonds.

    • A graphics glitch on "High Sierra", which could cause all atoms to appear at the centre of the screen, has now been resolved.

    • Addressed an issue with the Distance Explorer which could cause a crash when the Remove Duplicate Distances checkbox was set.

1. New Selection Commands. Two new selection commands have been added, making it easier to work with complex crystals and to select coordination environments.

   • The new Select Fragment command selects all visible atoms that are directly or indirectly bonded to the current selection; unlike the (similar) Select Molecule command, the selection does not propagate via hidden atoms or bonds.

   • The new Select Nearest Neighbours & Bonds command works like the Select Nearest Neighbours command, but also selects any bonds that are directly connected to any selected atoms. Note this command can be used iteratively, to progressively highlight 1st, 2nd, 3rd … N-th nearest neighbours.

   These commands are presented on the Edit > Select submenu, the Graphics Pane's contextual menu, and in the Selection Inspector's Actions menus.

2. Turbo-Charged Bonds Inspector. The Bonds Inspector has been redesigned to make its operation more intuitive, informative and considerably faster.

   The "+" button to add new bond specifications is always visible - except when the list fills the vertical space available (one can then add a new bond using the contextual menu). By default, all new bond specifications are blank; this is to avoid lengthy delays when working with massive (100,000+ atom) structures, where generating an arbitrary - and probably unwanted - set of bonds is undesirable.

   Adding new bonds to massive structures consisting of several hundreds of thousands of atoms is at least two orders of magnitude faster, thanks to the use of our "Turbo Bonds" algorithm to provide rapid coordination number summaries.

   When working with large structures, adding a new bond causes a status sheet to appear during the course of the operation, thereby making it clear that the program is indeed working and hasn't frozen up.

3. Improved Distances Explorer. Loading distances for massive structures is now 2-3 times faster thanks to improved algorithms and greater use of multi-processing. For very large structures, a default (and potentially time-consuming) distance search is suppressed, leaving you to choose which distance(s) to display. For smaller structures (< 10,000 atoms) a default search is retained.

   The Distances Explorer also now performs its searches in the background, allowing a progress bar to be displayed.

4. Faster Atoms Inspector. When working with a massive structure, changing atom colours, element type or polyhedral styles could cause the program to become unresponsive. A new cacheing algorithm now lets the operation proceed in a few seconds, instead of many minutes.

5. Expanded Documentation. A new, 26-page chapter, Chapter 6: Models has been added to the User's Guide (Help > CrystalMaker User's Guide). This covers the different model types available, including how to change the styles of different model elements via the Model Inspector, as well as rendering the model: background shading, depth fading, reflectance, etc. - which are controlled in the Rendering Inspector.

   Online Help (Help > CrystalMaker Help) has also been expanded and comprehensively re-indexed. A new hierarchical section on Selection has been added, including details of the new Select Fragment and other commands.

6. VMWare Compatibility. This version of CrystalMaker X now runs in virtualisation environments such as VMWare, where the Apple Software Renderer is used in place of hardware acceleration.

7. Miscellaneous Changes. This version includes numerous performance and interface enhancements plus bug fixes.

   • This version improves compatibility with Intel Integrated Graphics chipsets with limited 3D texture capabilities and/or video RAM. This should prevent graphics corruption (grainy textures, missing or clipped atoms, etc.) and/or crashes. We should emphasize that such issues were only experienced on some lower-specification Macs (generally laptops) which lacked dedicated graphics cards.

   • The (optional) toolbar scaling buttons are now continuous. (These buttons can be added to the toolbar by right-clicking and choosing the Customize Toolbar command.)

     Note that the action is not quite as smooth as we would like, as for this type of toolbar control the "repeat action" operates at a system level - and is determined by the "Key Repeat" rate, as shown in the Keyboard pane of the System Preferences Panel.

   • Added a new Spin All command, which starts all documents auto-rotating. To use this command, hold down the shift key and choose Transform > Spin (or click the Toolbar's Spin button).

   • The Set View Direction command now applies to all visible structures, rather than just the primary selection. As a result, oriented interfaces and other multi-structure views now behave consistently.

   • Live Rotation between CrystalMaker X and SingleCrystal 3 is now much smoother than before.

   • The Show in Atoms Inspector command on the Graphics Pane's contextual menu now works correctly.

   • Toggling atom visibility now longer changes bond radii. Bond radii are now based on the smallest atom in the structure, regardless of the atom's visibility.

   • The Bonds Inspector now allows multiple specifications to have their Label checkbox toggled. Simply select multiple rows, then click the Label checkbox in one of the selected rows.

   • Changing Primary/Secondary status in the Bonds Inspector now results in coordination polyhedra being regenerated.

   • Changes to the way in which the Define Cluster popover's combo box is initialized mean that loading any document is now considerably faster. Massive structures, in particular, provide much snappier display, because of greatly-reduced system overhead.

   • Choosing File > Save and then cancelling no longer results in the command becoming greyed out.

   • A rare bug with the Calculate > Plane Through Points command has now been fixed. In certain cases, the displayed plane was offset very slightly from the centre of selection (even though the plane's calculated centroid was correctly indicated).

   • Structures List thumbnails can again be dragged-and-dropped from one document to another. (This action stopped working in version 10.0.7, apparently due to Apple compiler changes in Xcode 9.)

   • Improved algorithm for displaying multiple unit cell frames.

   • The Show Legend preference now works correctly.

   • PDB files with (non-standard?) hexadecimal atom serial numbers are now imported correctly. The hexadecimal numbers are now (correctly) converted to integers.

   • LAMMPS files containing arbitrary atom column positions can now be read.

   • Chem3D and CCL files containing DOS line breaks (CR+LF) can now be read correctly.

   • Fixed a display glitch whereby newly-created thermal ellipsoids (defined using the Edit > Crystal command) were drawn at incorrect sizes.

   • Line widths in exported graphics are now rendered more consistently.

   • Structures imported from a text file are now correctly auto-scaled.

   • Added a workaround for a scaling issue on macOS 10.13 "High Sierra". A spurious rescaling event occurs when a document is loaded, which caused the first structure of a multi-structure document to have its scale reduced compared to the remaining structures.

1. Improved Graphics Compatibility. CrystalMaker for Mac now performs more diagnostic tests on startup to try to detect whether the current video card is capable of providing the requisite level of accelerated graphics. As a result, the software can fall back from its preferred (OpenGL 4.1) graphics mode to a compatibility mode (OpenGL 3.2).

   Whilst similar tests were indeed made on earlier versions of the software, it transpired that some video cards - and all Intel "Integrated Graphics" chipsets - were misrepresenting their capabilities, fooling the software into assuming that some graphics operations were possible when they were in fact not implemented on the video card. Such devices caused various graphics glitches including missing or incorrectly-drawn bonds and general "weirdness".

   CrystalMaker displays information about the current graphics capabilities and runtime modes in each document Log pane. The program is also now capable of running with Apple's Software Renderer, allowing it to run in VMWare

2. Faster Loading of Massive Structures. A more efficient Legend-generation algorithm is now used, allowing significantly-faster loading of massive structures.

3. Reduced Memory Requirements. The Library Browser has been optimized to require considerably-less memory. New thumbnails are generated using more compression and stored in a more efficient manner.

4. Expanded User's Guide. The CrystalMaker User's Guide has been greatly expanded with two new chapters, covering "Building Crystals" and "Building Molecules". These are highly-detailed chapters which have been entirely rewritten for the new software and should provide the definitive reference to using the program.

5. More-Comprehensive Menus. Many commands which were previously only available via a contextual menu, or in the Selection Inspector's Actions menus, have now been included on the main menu bar. These include commands for extending a selection (e.g., nearest neighbours, ring, molecule etc.) which have been added to the Edit > Select submenu. Menu titles have been clarified and their layout improved, in order to make it easier for users to browse them more logically.

6. Improved Space Groups Popover. This is now wider and taller, allowing all columns to be browsed without the need for horizontal scrolling.

7. Greater Tolerance of Poorly-Formatted PDB & Molfiles. PDB files with (erroneous) zero site occupancies can now be loaded and are auto-corrected. PDB files with dummy 1 ų unit cells are now loaded as molecules, thereby avoiding a potential freeze caused by over-generation of (physically-unrealistic) bonds. Molfiles with incorrectly-defined bond fields are now auto-detected and loaded.

   These changes were made to help users working with badly-generated files produced using certain well-known third-party programs. We do not condone such sloppy formatting, and encourage other software developers to properly implement file formats in future.

8. Miscellaneous Changes. This version includes minor enhancements and bug fixes.

   • Added OpenGL diagnostic information to the window log. This shows the current graphics renderer, its OpenGL version - and indicates whether the program is being run in compatibility mode (OpenGL 3.2) or using latest graphics (OpenGL 4.1)

   • Changed the default graphics export format (File > Export Graphics > 2D Graphics) from PDF to PNG. The latter command works really well and gives exceptionally-high-quality output with the option of transparent backgrounds. As with all other OpenGL-based programs, PDF graphics are not recommended because of their massive size (huge numbers of triangles).

   • Thumbnail generation for text files in the Library Browser is now disabled by default - but can be enabled using the Preferences panel.

   • Added an (optional) Labels button to the toolbar. This button - which can be added by customizing the toolbar - toggles all atom labels on or off.

   • Added a New Empty Molecule command to the window's Add menu and the File > Add to Window menu.

   • The Calculate > Distance from Plane command now works in cases where a document contains one or more molecules.

   • Using the Zapper tool now updates the legend.

   • When loading structures from a text file, the filename is now used to name the individual structures. (Apart from CIF files, where individual data_ tags are used.)

   • Improved vector graphics output: line widths are now more consistent.

   • Editing the unit cell parameters in the Crystal Editor now correctly redraws the structure.

   • Editing site occupancies in the Crystal Editor now correctly updates individual atoms on screen.

   • A graphics glitch involving transparency (introduced in version 10.0.6) has now been resolved.

   • Resolved an issue with synchronizing molecules: orientations are now correctly applied.

   • Entering non-RGB colours (e.g., CMYK or greyscale) no longer causes a crash.

   • The Distance Explorer window now opens correctly on Mac OS X 10.10 Yosemite.

   • Implemented the Show in Atoms Inspector command on the Graphics Pane's contextual menu.

   • Changing atom visibility no longer changes bond radii; these are calculated on the basis of the smallest atom in the whole structure - not just the visible atoms.

1. DEN Volumetric File Import. ".den" data files (as generated by the MEED/PRIMA and derivative programs) can now be opened in CrystalMaker X. The files can also be imported into an existing structure, via the Add popup menu in the Volumetric Datasets group of the Model Inspector.

   CrystalMaker X can load multiple volumetric datasets from the same ".den" file (up to a maximum of 5 datasets).

2. Faster Graphics. When the "Fast Graphics" mode is in operation, rotations and animations are further accelerated, thanks to changes to the number of transparency levels used. This change also affects Retina displays and means that full-screen 5K pixel-doubled animations can now be played at twice the speed of earlier versions.

3. New Tutorials. The new "Tutorials" link on the Help menu opens a new PDF document with two separate tutorials. A new tutorial has been added here, which provides a very-detailed introduction to the process of building a new crystal structure from scratch, adding bonds and polyhedra, changing styles, using multiple lattice planes to define a slab, and exporting high-resolution graphics.

4. Drag-and-Drop Loading of Images. Background images can now be dragged-and-dropped into the Graphics pane. As a result of this change, we have removed the "image well" from the Background group of the Rendering inspector.

5. Miscellaneous Changes. This version includes minor enhancements and bug fixes.

   • Improved vector graphics output: this results in slightly-smaller file sizes and faster output. In addition, stylized thermal ellipsoids are correctly rendered to PDF or EPS formats.

     Please note, however, that vector output will always be vastly slower than pixel graphics: this is an inevitable consequence of the high-quality graphics rendering used by CrystalMaker X. We strongly recommend that you use high-resolution pixel graphics, as this will give vastly-superior quality (including transparent backgrounds) and is much, much faster to generate. Vector graphics should only be used for very-basic "line art" output.

   • The threshold steppers in the Volumetric Datasets group now provide much finer control.

   • Fixed an issue with the Distances Explorer (introduced in version 10.0.5) which prevented some distances from being displayed correctly.

   • Improved the Auto Centre command to use the centre-of-gravity of the structure, rather than a rectangular plot range.

   • Synchronizing crystals with lattice planes now correctly updates the plane orientation.

   • Fixed an issue with lattice planes not being saved correctly after a structure has been rotated.

   • Fixed an issue with unit cell axes appearing and disappearing during the course of a multi-structure animation.

   • Structures imported from CMTX files can now be displayed in Thermal Ellipsoid mode.

   • Organic molecules containing terminal halogen atoms can now be correctly relaxed.

   • Fixed a rare bug with the Crystal Editor and rhombohedral space groups, in which attempting to edit the α angle caused the space group to revert to its hexagonal setting.

   • Fixed an intermittent problem with the calculation of coordination numbers, which could prevent certain bonds from being generated.

1. Improved Graphics Quality and Compatibility. Users with older Macs will see major improvements in the graphics in this version. There are two key changes:-

   Firstly, we have added the ability to switch graphics compatibility between the default option (OpenGL 4.2) and a fallback option (OpenGL 3.2). The fallback option may improve compatibility with older graphics cards - albeit with slightly slower performance. (We have encountered some Mac graphics card which claim to provide advanced OpenGL 4 capability, but fail to deliver, resulting in missing bonds or vectors; in these cases, switching to the OpenGL 3.2 graphics should fix any display issues.)

   Secondly, users with older, non-Retina, displays, will see smoother graphics. CrystalMaker also offers the option of a "Fast Graphics" mode, in which standard-resolution graphics are used during rotation and scaling, with the structure redrawn at high resolution (and smoothing) when idle.

   These two new graphics options can be controlled via the new Graphics pane in the Preferences panel.

2. GRD Volumetric Support. GRD volumetric data files can now be opened in the program - or added to an existing structure's Volumetric Datasets list. These files can also be exported.

   GRD files are very-similar to CrystalMaker's own generic "Voxel" format - but they also include unit cell dimensions, meaning that the files can be opened on their own (in which case, a dummy crystal structure is generated).

3. Drag-and-drop Loading of Volumetric Data. The Volumetric Datasets list in the Model Inspector now accepts drag-and-drop. Providing you use the standard file extensions (e.g., ".grd", ".vox", ".castep", etc.), you should be able to drag-and-drop volumetric data directly into the list, for instant display.

4. Miscellaneous Changes. This version includes minor enhancements and bug fixes.

   • This version uses a more-efficient algorithm to save crystal structures in a document, which reduces file sizes quite considerably. (This change has no effect on molecular structures.)

   • The formula string in the Info Inspector is now correctly formatted for molecules. (The earlier version simplified the formula, giving relative, rather than absolute element proportions.)

   • Fixed a unit cell display issue when the unit cell range is very small.

   • Fixed a problem with legacy graphics (OpenGL 3.2) which prevented vectors from being drawn correctly.

   • Added an additional "undo" step so that a multi-structure synchronization operation can now be undone.

   • Hiding atoms now updates the Info Inspector.

1. Merge Structures. Multiple structures can now be merged into a single structure. This works for any combination of crystals or molecules. The primary selection is treated as the host structure and any visible atoms from the other structures are copied into the host structure. If the primary selection is a crystal, you will be prompted to discard the symmetry.

   This command is similar to the "Place Molecule" command found in earlier versions of CrystalMaker, but is better, because it allows multi-structure merging (including molecules merged into crystals) and allows experimentation - via separate structures in the same window - prior to merging.

2. Major Performance Improvements. Automatic bond generation is now significantly faster - up to 12x faster for massive structures with low-symmetry (e.g., DL_POLY files).

3. Faster Synchronization. Synchronizing massive structures is now significantly faster, thanks to smarter search algorithms. For example, the time taken to synchronize 500 structures with 3600 atoms in each structure (1.8 million atoms total) was reduced from 123 s to just 23 s (over 5x faster) in our tests.

4. Improved Video. Video output at high frame rates is now of much higher quality than before. A progress bar is shown for the video recording, with a cancel button. When exporting an animation, the current animation settings (which can be edited by clicking and holding down the toolbar's Play button) are now used as the movie settings.

5. Revised Atom Selection Actions Menu. The Atom Selection group in the Selection Inspector has a revised Actions menu (the cog icon on the top right-hand side of the group). This includes new commands to print information in the window log. For example, atom information will include fractional and orthogonal coordinates, the thermal ellipsoid tensor and its principal axes, plus the volume of any coordination polyhedron around the selected atom.

6. Miscellaneous Changes. This version includes minor enhancements and bug fixes.

   • The Info Inspector now displays whether the current structure (primary selection) is a crystal or a molecule.

   • Added a new Clathrates folder to the "Hybrid Materials" section of the Structures Library.

   • Added Folder Tips to the remaining folders in the Structures Library. (Hovering the mouse over a folder will display a help tag with information about the contents of that folder.)

   • Graphics are automatically updated when a window is dragged from one screen (e.g., a Retina display) to another screen (e.g., a regular display).

   • The Auto-Scale and Auto-Centre commands can now be used during the course of an animation: all structures in the animation are updated.

   • Dragging-and-dropping a text file into an existing document now displays a progress bar during loading.

   • Updating the probability value for thermal ellipsoids (via the Model Inspector) is now smoother and more reliable. Earlier versions of the program attempted to scale existing ellipsoids; the current version now recalculates the ellipsoids from scratch, which is more reliable and does not require information about previous sizes or scales.

   • Structural data split between different loops in the same CIF file are now read correctly.

   • Fixed a display issue with thermal ellipsoids, which resulted in anisotropic ellipsoids appearing slightly distorted.

   • When using the Symmetry Explorer to customize symmetry, clicking the Apply button now correctly updates the symmetry in the Crystal Editor.

   • Fixed a minor glitch in the Bonds Inspector coordination previews for molecules: the coordination details for the "to" atoms are now correctly updated.

   • Deleting an unselected structure using the Structures List's contextual menu now works correctly (i.e., the structure to be deleted does not need to be selected).

   • Fixed a problem which could cause a crash when loading a document whose filename was greater than 80 characters in length.

   • Fixed a problem with the listing of some bond angle results in the Log: certain angles were written as obtuse rather than acute.

   • The Transform > Unit Cell > General Transformation command now works correctly: a window sheet is displayed, allowing you to enter a transformation matrix, or choose from a number of preset transformations.

   • The Discard Symmetry command now correctly resets the spacegroup origin choice - if the original structure had a dual-origin spacegroup.

   • Structures Library documents opened from the Library Browser are no longer marked as "changed" by default. This makes it easier to quickly open and close library files without being reminded to save new documents.

1. Ring Selection. It is now possible to select all atoms in a structural ring (e.g., a benzene ring) by selecting one atom in the ring, and choosing the Extend Selection > Ring command from the Graphics Pane's contextual menu.

   This command selects the shortest-possible ring that passes through the selected atom. If multiple rings (of the same dimension) pass through the atom, the first ring is selected, but data for each ring are presented in the Log pane: these include the ring path, the ring orientation (best-fit plane through ring points) and the ring's centroid.

2. Merge Command. A new command has been added to the main menu bar (Transform > Selection > Merge) and to the Graphics Pane contextual menu. This allows two or more selected atoms to be merged into a single atom or site. This is especially useful when working with disordered structures.

   For example, consider a structure where a carbon atom is on a so-called "split site", i.e., disordered between one of two closely-spaced positions. The resulting structure would show two carbon atoms (each with a 50% occupancy) instead of one - plus extra chemical bonds. One might wish to neaten this up, by showing the average position of the atom. To do this, one would simply select the two closely-spaced atoms and choose the Merge command. The two carbon sites would then be replaced by an average site - and, if this is a crystal structure, the result would be propagated throughout the crystal lattice, resulting in a much neater and easier-to-understand structure.

3. Library Browser File Tips. Tool tips are displayed when the mouse hovers over any item in the Files pane. For document thumbnails, the title and chemical formula is shown. For folders, a descriptive note is shown, which explains the contents of the folder.

4. Improved Selection Inspector. If multiple atoms are selected, their centroid is now displayed, together with its average bond length. For single-atom selections, any hidden or secondary bonds, are clearly identified. The average bond length now only refers to primary bonds.

5. Improved generation of planar polyhedra. A new algorithm makes is easier for the program to detect planar environments, resulting in a neater display (compared to earlier versions of the software, which would try to generate highly-flattened polyhedra).

6. Improved chemical formula display. Organic structures now have their formulae presented according to the "Hill" convention, with Carbon first, then Hydrogen (if present), followed by the other elements in alphabetical order. For inorganic structures, the cations are given first - with Al and Si arranged next in the list - and with anions last.

7. New Structures. The Structures Library has been reorganised. A new "Hybrid Materials" folder has been added, containing Molecular-Organic Frameworks (MOFs) and Zeolitic Imidazolate Frameworks (ZIFs). A new "Inorganics" folder is subdivided into Minerals and "Other Inorganics" - with the latter subdivided by chemical classification. A number of new crystal and molecular structures have been added.

8. Miscellaneous Changes. This version includes minor enhancements and bug fixes.

   • For greater clarity, the Arrow tool no longer highlights bonds to hidden atoms.

   • Holding down the shift key now lets one reapply an existing plot range - with the Range popover. This might be useful to force a recalculation of the structure, or to ensure that all atoms and bonds within that range are made visible.

   • Added a new Registration dialog, to encourage new users to register their details when they first licence the software.

   • Changing the visibility of a selection now automatically results in the remaining structure being auto scaled.

   • A new, Symmetry-Related Bonds command has been added to the Extend Selection submenu of the Graphics Pane's contextual menu.

   • Removed the default assignment of a CrystalMaker text icon for blank document types. CrystalMaker can open documents without file type information and/or file extensions and, by default, we specified a standard CrystalMaker icon for such file types. However, some users found that unrelated files, such as UNIX executables, were shown with these icons, which was undesirable. This is not a bug - it is simply the way the Mac works: the newest application to be installed is used by the system for assignment of file icons.

   • Dragging-and-dropping multiple documents onto the application icon now correctly results in multiple windows being opened.

   • Changing the current tool (from the tool strip) in one window now results in other document windows having their tool strips updated.

   • Fixed a (very rare) problem with planar polyhedral faces being drawn incorrectly.

   • CIF files with (invalid) blank data headers can now be loaded. The resulting datasets shown as "Untitled".

   • Dragging a structure thumbnail from one window to another no longer results in corrupted symmetry.

   • The Add/Delete Bonds tool now works correctly, irrespective of the order in which the two bonded atoms are chosen.

   • Polyhedral overlays now vanish when the scale is changed or a structure is rotated. This is to prevent "ghosts" remaining on the screen.

   • Thermal ellipsoids drawn using "ORTEP-like" styles now have consistent line widths for equatorial and outline markings.

   • Fixed issues relating to a bond's primary/secondary status being changed. The program now recalculates coordination numbers and polyhedra accordingly.

   • Fixed a rare issue reading from older CrystalMaker 7-9 files with blank or invalid data strings.

1. New Quick Tour Videos. A series of new Quick Tour videos have been added in this release, including Lattice Planes, Selection and Measurement. All videos have been re-edited to make them shorter and better focused. (Note: If the Quick Tour window doesn't open when you launch the program, choose: Help > Quick Tour to display the tours.)

2. Improved Chemical Formula Generation. Formula proportions are now scaled according to their greatest-common-denominator. The order of the elements now matches the "Hill" system (listing Carbon and Hydrogen first, followed by the other elements in alphabetical order).

3. Miscellaneous Changes. This version includes minor enhancements and bug fixes.

   • The Graphics Exporter panel now allows a wider range of magnifications, using the new magnification field.

   • Atom, bond and polyhedral previews are now shown at very-high resolution.

   • CrystalMaker now launches correctly on Mac OS X 10.11 "El Capitan" - albeit without the Quick Tour window (this is a workaround for a bug with Apple's web viewer). To view the Quick Tour, choose: Help > Quick Tour, whereupon the tour will commence in the Safari web browser.

   • DL_POLY "Config" output now works correctly: the exported coordinates match the exported orientation matrix. In addition, the atom label field now contains just the element symbol, as required by the file format.

   • Polyhedra are now generated using only primary bonds. Secondary bonds - which could include inter-molecular bonds and/or any distance measurements - are excluded from polyhedral generation and coordination number calculation.

   • Scroll-wheel zooming now works correctly when animating; all frames of the animation will be correctly scaled.

   • Improved stability on Mac OS X 10.10 and 10.11, following fixes to an issue involving scale changes and the window ruler.

1. Quick Tour. A new window appears when the program is launched, providing a series of quick video tours to the program. This can be hidden if required and displayed later via the Help > Quick Tour command.

2. Set Plot Size command. A new Window > Set Plot Size command allows a precise size to be specified for the Graphics Pane. This is useful when saving video or precisely-sized graphics.

3. New Help links. Help commands have been added to contextual menus for the Structures List, the Tool Strip, plus the Distance Explorer and Vibrations Explorer windows. A new Help button has also been added to the View Direction sheet.

4. Miscellaneous Changes. This version includes minor enhancements and bug fixes.

   • Added a contextual menu to the Graph Pane of the Vibrations Explorer.

   • Added command-key shortcuts for the various model types on the Model menu.

   • Dragging a Structures List thumbnail into the Graphics Pane of another window now makes the resulting new structures visible in the destination Graphics Pane.

   • Editing a structure now updates the coordination previews in the Bonds Inspector.

   • Fixed a minor glitch with unit cell editing fields not remaining hidden after an unconventional space group symbol had been entered into the Crystal Editor.

   • Toggling the Grid and/or Axes now works correctly in the Vibrations Explorer window.

CrystalMaker X is an entirely-new program, developed from scratch for the very-latest Mac and Windows operating systems. Every line of code has been rewritten, with an entirely-new, object-oriented architecture, brand-new OpenGL-based graphics engine, new interface design, and a new, fully-integrated, structures library.

1. State-of-the-art design. CrystalMaker X is a state-of-the-art, 64-bit multi-processor, multi-touch, multi-structure application.

   • Object-oriented design using native Objective-C/Cocoa code.

   • 64-bit precision used for all calculations and storage.

   • Multi-processor design for improved performance.

   • Multi-touch rotation, zooming and scrolling with a trackpad.

   • Drag-and-drop structures between windows.

2. Built for Mac. CrystalMaker has always been a native Mac program. And the results speak for themselves:-.

   • Retina display: gorgeous high-resolution graphics on the latest Macs.

   • Full-screen mode including "Spaces" support.

   • Supports document tabs in macOS 10.12 "Sierra".

   • Dedicated Touch Bar interface (MacBook Pro) with powerful controls for rotation, scaling, animation, structure building and measurement.

   • Quick Look thumbnails and previews, including multi-structure previews.

   • Security-compliant sandboxed application: works with system "Gatekeeper" to help keep your Mac safe from malware and viruses.

3. Beautiful New Interface. The program was designed to maximize your productivity, by placing controls at your fingertips, but without crowding the interface. The Structures List, Log and Inspectors are all available in the main document window (and can be toggled open or closed). In addition, much functionality is available via popover windows, including plot range, cluster control, rotation angles, animation settings.

   • Integrated document window with Structures List, Inspector, Log and toolbar.

   • Library Browser with animations, structure rotation - and a search command.

   • Symmetry Explorer.

   • Packing Explorer: design molecular crystals in real time.

   • Vibrations Explorer: animate vibrational modes & IR spectrum.

   • Preferences window with Elements Explorer and Periodic Table display.

4. Stunning Graphics. CrystalMaker X uses an advanced new graphics engine, based on the industry-standard OpenGL but optimized to deliver class-leading rendering with unsurpassed transparency effects. Both Mac and Windows versions support high-resolution ("Retina") displays and offer flexible output options.

   • Pixel-perfect OpenGL graphics. Complex intersections between multiple objects (e.g., spheres and planes or polyhedra) are accurately rendered.

   • High-performance. Take advantage of graphics acceleration on your computer's graphics card to speed manipulation.

   • Customizable reflectivity and up to 4 light sources.

   • High-DPI "Retina" display on Mac (iMac and MacBook/Pro with Retina display) and Windows (e.g., Microsoft Surface Pro).

   • Rich-text annotations with subscripts and superscripts. Change fonts, colours, styles, sizes and baselines (super/subscripts) within any annotation, for beautiful captions and titles.

   • Vector graphics output using PDF and EPS (Mac) or WMF (Windows).

   • Export high-resolution graphics with transparent backgrounds. TIFF and PNG files have the option of using a transparent background.

5. Real-Time Editing. CrystalMaker X's integrated inspectors make structure editing a breeze.

   • The Info pane displays rich-text notes plus detailed structural information such as chemical formula, numbers of visible atoms, symmetry, etc. - which are updated on-the-fly.

   • The Atoms inspector displays all of the atoms or structural sites, grouped by chemical element (or by molecule, or ungrouped, if required). Clicking on the atom preview displays a popover for editing sphere, ellipsoid or polyhedral styles. Multiple rows in the can be selected to speed up editing. A contextual menu provides powerful commands, including automatic colouring and the ability to switch between preset atomic radii sets.

   • The Bonds Inspector combines bond specifications with style control - and automatic labelling. Coordination information is displayed on the right-hand side.

   • Model & Rendering inspectors let you adjust all aspects of your model's display. Contextual menus in each control group let you customize your preferences, reset styles, or apply the current settings to all structures in the document.

   • A Selection inspector is displayed whenever one or more objects (atoms, bonds, polyhedra, annotations, vectors) are selected. You can simply point and click on an object, then use the Inspector to edit the object's settings. The Inspector changes, depending on what is selected. Powerful "Actions" popup menus allow you to propagate your changes to symmetry-related atoms or bonds, isolate your selection, and much more.

   • A new Cluster button, in the window toolbar, lets you edit a spherical cluster interactively: changing the centre point and its minimum and maximum radii.

6. Multi-Structure Visualization. CrystalMaker X is a multi-structure application, allowing you to display unlimited numbers of structures in the same window, at the same time.

   You can opt to treat the structures as a sequence, switching between separate structures to make a slideshow or animation - but you can also have multiple structures displayed simultaneously on the screen, simply by selecting them in the program's Structures List (command-click for multiple selections). This is an ideal way to work with interfaces, surfaces, or simply to compare two or more structures "superimposed", as the images overleaf illustrated.

   • Drag-and-drop structures between windows.

   • Fast multi-structure animation.

   • Compare differences between two or more structures on screen.

   • Create multi-structure crystal interfaces without having to merge them.

   • Rotate animations in real time.

   • Multi-structure synchronization with atomistic-level control.

7. Flexible Bonding. Responding to customer demand, we have introduced a wide range of new bond styles including double and triple bonds. A new "thin" bond style - distinct from the line styles - offers greater flexibility for showing weaker or hydrogen-bonded interactions. In addition, bonds can be defined as primary (the default option) or secondary bonds; secondary bonds are designed to illustrate inter-molecular interactions, and are ignored by the molecular crystal isolation commands.

   • 14 stylized ("2D") and 10 photo-rendered ("3D") bond styles.

   • Double-, triple-, segmented- and dotted-bonds.

   • Primary or secondary bonds.

   • Bond distance labels.

   • Thin bond cylinder option.

8. Powerful Polyhedra. CrystalMaker X provides powerful polyhedral display options and customization.

   • Concave polyhedra with curved faces.

   • Ellipsoids in polyhedra.

   • Control over polyhedral frame widths.

9. Multiple Lattice Planes. CrystalMaker X allows unlimited display of multiple lattice planes/sets:-

   • Multiple lattice planes.

   • Parallel lattice plane sets.

   • Display of symmetry-related planes.

   • Automatic lattice slab generation.

10. New File Formats. CrystalMaker X can read from 8 new file formats, some of which comprise a range of flavours:-

    • CASTEP Cell

    • CASTEP Volumetric (chdiff_fmt, den_fmt, elf_fmt formats)

    • CASTEP Output (includes all frames in the trajectory)

    • Gaussian CUBE

    • DL_POLY Config and Revcon formats (plus existing History import)

    • GULP (loads input, output structures plus any volumetric data)

    • RMCprofile

    • VASP Volumetric (ELK, CHK, CHGCAR)

    CrystalMaker X can export data to 4 new file formats:-

    • CASTEP Cell

    • DL_POLY Config

    • RMCprofile

    • VASP

11. Packing Explorer. Turn any molecule into a molecular crystal.

    • Rotatable preview with customizable model type.

    • Rotate molecule relative to cell.

    • Edit molecular placement.

    • Edit symmetry.

12. Symmetry Explorer. Browse symmetry relationships in 3D with this new window. You can choose any spacegroup, or define your own symmetry elements and visualize how they affect a structure.

    • Visualize general-equivalent positions in 3D, with cell dividers and full rotation control.

    • Space group popover, with preview.

    • Slider controls to edit the general-equivalent position (e.g., to move to a "special" position).

13. Volumetric Data. CrystalMaker lets you visualize volumetric data imported from text files, or generated within the program in electron density or porosity calculations.

    • Visualize CASTEP, Gaussian CUBE, GULP, VASP and Voxel files.

    • Visualize porosity as "negative" (void) or "positive" (filled) space.

    • Calculate and visualize electron density for any crystal.

    • Clamp data display range using slider controls.

    • Work with multiple datasets in the same window.

14. New Simulation Engine. CrystalMaker X has a redesigned simulation engine for faster and more-accurate output, letting you build and relax molecular structures and calculate their vibrational properties.

    • True energy-minimization algorithm (not just structure optimization).

    • Calculate energy for any molecular structure.

    • Extensive new potentials library for a wide range of bonding configurations.

    • Two-stage process: Monte Carlo followed by Least Squares for greater finesse.

    • Simulates vibrational modes (eigenvectors) and their frequencies.

    • Infra Red spectrum display.

    • Visualize vibrational modes with real-time rotation and scaling.

15. Integrated Structures Libraries. The Library browser lets you find structures quickly and easily, providing a single location for your recent files, favourite items, program examples - and our very-extensive reference library. The Library Browser is available as both a standalone window (via the View menu) or as a sheet window, via the toolbar's Add popup.

    • Integrated reference library with 1000+ structures.

    • Integrated examples library.

    • Browse recent files.

    • Organise your own structures into custom folders.

    • Automatic thumbnail generation for CIF and other text files.

    • Search by title, notes, chemical formula.

    • Interactive previews with auto-rotation and animation.

16. Other New Features. CrystalMaker X has many more enhancements which will become clear as soon as you start using the program. However, here are just a few to whet your appetite.

    • Rotatable Distance & Angle Measurements. You can now rotate and scale your structure without losing your Bond Distance, Bond Angle or Torsion Angle measurements.

    • Labelled Bond Distances. Bond distances can now be preserved as "Distance Measurements" (which are secondary bonds, displayed with a dotted line style) with the bond distance shown alongside.

    • New atom styles including defect symbols and emoji styles.

    • Colour-by-Molecule command.

    • Van-der-Waals surfaces. Add a surface to your structure with a choice of existing element radii, or Van-der-Waals radii.

    • Solvent-excluded surface. A powerful surface overlay option with customizable "probe sphere" radius, letting you visualize your structure in new ways.

    • Legend. A key to the atoms in your structure, the Legend can be dragged to different parts of the window or hidden entirely.

    • Preserve molecular coordinates as you rotate.CrystalMaker provides both screen coordinates and your original structural coordinates.

    • Flexible range generation: specify whatever range limits you require, without them being reset (earlier versions of the software required all range limits to start at the origin, resetting negative values; the new program has no such limitations).

    • Calculate Molecular Centroids command generates dummy atoms at the centres of each molecule. You can use these as proxies for the molecules in a complex molecular crystal, hiding the actual molecules and focusing on how their positions (centroids) change during the course of an animation.

    • Least-squares best-fit plane through points.This improves on previous versions of the program and gives consistent, accurate results.

    • Best-fit line through points.This allows you to calculate the orientation of a selected group of atoms.

    • Emphasize front cell edges.Sometimes it is difficult to infer which edges are the front edges, and which are the back. With the Emphasize Front Edges option in the Model Inspector, the front edges are emphasized with thicker lines than the back edges, thereby making the cell orientation clearer.

    • Coloured unit cell faces.Whilst the unit cell is generally represented by its edges, you have the option of displaying its faces in any colour and transparency.

    • Selectable bonds.Simply click on any bond with the Arrow tool and it will appear selected. The bond properties are then displayed in the Selection Inspector, for easy editing.

    • Edit bond specifications from a selected bond. You can edit the properties of any selected bond (in the Selection Inspector) and then apply your changes to all bonds which share the same bond specification. Alternatively, you can select a bond and use the Selection Inspector's Show in Bonds Inspector command to go directly to the corresponding bond specification.

    • Select symmetry-related bonds. The Selection Inspector lets you take any selected bond and offers the option of selecting all symmetry-related bonds.

    • Selectable atom rows in the Atoms Inspector. One or more rows can be selected (command-click to make a discontinuous selection) in the list; you can then use the contextual menu to select the corresponding atoms on the screen.

    • Perspective grid. When perspective is in effect, the grid changes to show the walls of a bounding box, emphasizing how scale varies with depth.

    • Atom search. You can search for an atom or site label in the current structure. If found, the corresponding row of the Atoms Inspector is selected. You can also search for an individual atom by entering its atom number in the search field. If the atom is visible, it will be marked selected, and its properties displayed in the Selection Inspector.

    • Axial vectors can be dragged to different parts of the screen.

    • Width and height of rectangular selection is displayed when you click-and-drag with the Arrow tool.

    • Add Title command. You can have a structure's name automatically displayed as a new annotation object, using this command from the Model menu. The title is displayed in one of six positions in the graphics pane (which you can customize using the Preferences panel). Holding down the shift key adds titles to add structures in the Structures List: invaluable when working with many frames from a simulation or structure sequence.

    • Edit position and size of annotations by entering numeric values in the Selection Inspector.

    • Edit atom or site labels directly in the Atoms Inspector (or Site Inspector), without having to use the Crystal or Molecule editors.

    • Separate Bond Angle & Torsion Angle tools. Owing to public demand, we have reinstated the Torsion Angle Tool as a separate tool in its own right. (In CrystalMaker 9 this tool had been merged with the Bond Angle tool.)

    • Create bonds using the Distance Tool. When measuring bond distances, a popup window allows creation of a bond using the Distance Tool.

    • Add Atom Tool with live distance display. Holding down the shift key when using the Add Atom tool displays a labelled preview of the bond to be inserted between the last-clicked atom to the current mouse position.

    • Smart "Bend Selection" command for nanotube generation; removes overlapping atoms.