These notes refer to a legacy product that is no longer supported. Please order your CrystalMaker 11 upgrade, and look forward to a new era of advanced chemical & materials modelling - plus our usual service and support!
Miscellaneous Changes. In this, our 42nd free update for CrystalMaker 8 in six years of continuous support, we are pleased to provide further improvements to the software, including an updated User's Guide, and miscellaneous service updates, as detailed below:
Fully Code-Signed Application. Whilst CrystalMaker 8 has been code-signed for a number of years, this did not include the "helper" applications included in the main application bundle. Those separate applications, which include the Spotlight Metadata Importer and the QuickLook Generator, are now all code-signed, for improved security.
Improved Dashed-Line Drawing. Monotone dashed lines now always start and end on a dash, making it easier to follow lines in "stick" or "wireframe" plots. This change also reduces the possibility of exported, high-resolution graphics, having superimposed line dashes "cancelling out" due to inverted phases.
Miscellaneous Changes. This version includes miscellaneous improvements and bug fixes:
Accelerated CIF Import. CrystalMaker now uses a much-faster algorithm for loading CIF files, which is orders of magnitude faster when reading massive files packed full of SHELX refinement data.
Improved CMTX File Import. CrystalMaker text files without explicit bond specifications (i.e., lacking BOND or BMAX cards) are now treated the same way as other text files, with auto-generation of bonds being the default (unless specified otherwise by the Transform > Generate Bonds at File Import option).
Miscellaneous Changes. This version includes improved file transfer for use with the diffraction commands:
Multi-Structure Rotation. The Auto Rotate sheet now allows auto-rotation for all windows, via a new checkbox option. This is useful for comparing two structures when their windows have been tiled.
Added New Spacegroups. Three new, unconventional, monoclinic spacegroups have been added: I 1 2/c 1, A 2/a 1 1, and B 1 1 2/b. These are all variants of spacegroup no. 15, C 2/c, but with interchanged axial settings.
Miscellaneous Changes. This version includes miscellaneous improvements and bug fixes:
Expanded User's Guide. The CrystalMaker User's Guide has been revised for this release and includes three additional Gallery examples, plus some illustrated Element Tables and more detailed descriptions of using the Lattice Plane tool.
Miscellaneous Changes. This version includes miscellaneous bug fixes for improved stability when opening a saved CrystalMaker binary file, or importing a VASP text file:
Indexed Online Help. The online help system is now indexed. Users can search for terms in the Help menu's search box, and a list of appropriate topics is displayed in the menu.
Miscellaneous Changes. This version includes miscellaneous bug fixes and a workaround for system changes on OS X "Lion" and "Mountain Lion":
Major New User's Guide. The Ninth Edition of the CrystalMaker User's Guide uses an all-new layout, aimed at making it easier for on-screen use. Extensive changes have been made to the content, adding two new chapters, new graphics, reorganising topics, and generally making the guide more accessible.
Partial "Retina Graphics" support. Extensive changes have been made to the user interface to provide "High DPI" support to all dialogs, sheets and virtually all palettes. The results can be seen on new "Retina Display" computers (e.g., Tools palette, Overview window, Elements window, etc.).
Please note that, for technical reasons, the Graphics window, Model Options, Rendering Options and Site Browser palettes, remain at standard resolution. However, we aim to provide full Retina Display graphics in a future version of the program.
DL_POLY 4 Support and Automatic File Naming. This version can now load 'History' files generated in the new, free-form DL_POLY 4 format.
When reading from a DL_POLY "History" file, CrystalMaker will now attempt to construct a more distinct filename, based on any information in the file itself, or the naming of its directory.
Redesigned Video Recorder & QTVR Options. The Video Recorder palette has been redesigned, with new icons and high-resolution preview. The QuickTime VR Options dialog has also been refreshed, with a new layout and preview. Both windows now support the Retina Display.
Miscellaneous Changes. This version includes numerous miscellaneous changes, including:
Show Molecular Cell Tool Button. The default toolbar now includes a handy shortcut for visualizing molecular crystals: the Show Molecular Cell button (abbreviated "Mol Cell").
This tool is designed for structures where there is no long-range bonding (i.e., those structures where discreet molecular groups are arranged within a crystal lattice, but without direct bonds between the molecules). The tool displays the contents of one unit cell, but optimized so that each molecular group is shown intact (possibly crossing the cell boundary).
This is a good way to start visualizing a molecular crystal; you can use the selection tools to further isolate individual molecules. (Note that this, and other related commands, are also available on the Transform > Optimize Range submenu.)
Scientific Notation Supported in CIF Files. CrystalMaker can now read data from CIF files which use scientific (Exponential) notation for floating-point numbers. Whilst such formatting is very rare - CIF files do not really require such extreme formatting - there are cases of machine-generated files using this formatting, and we are pleased to further strengthen our support for the CIF format.
Miscellaneous Changes. This version includes minor fixes to the Open Recent submenu and to file import:
Removed support for the use of the plus character ('+') to designate error bars in CIF files. This was used by the ICSD's 'Retrieve' program, but is not officially recognized in the CIF specification; instead, error bars should be designated using a pair of curved brackets, e.g., 2.341(1).
Changed the default window toolbar, removing the Range, Hide and Select popup menu buttons, to accommodate the new Show Molecular Cell button. Note that users can easily change the toolbar layout - and apply the default layout, or restore the popup menu buttons - using the Customize Toolbar command.
Reverse-Tabbing in Data Browsers. CrystalMaker now supports "backwards-tabbing" in all data browsers: hold down the shift key whilst pressing the tab key, to move the selected cell to the left.
Miscellaneous Changes. This version includes minor fixes to the Open Recent submenu and to file import:
The File > Open Recent submenu now works correctly when the Log pane (of the Overview window) is active.
When importing WIEN2k text files, the lattice type is now read.
Miscellaneous Changes. This version is now code signed and includes a revised licensing agreement:
All our Mac applications are now code signed, which will facilitate access for users running OS X "Mountain Lion" or later.
Our licensing agreement has been reworded to improve clarity and better differentiate our Personal licences from multi-user licences.
Improvements to VASP File Import. CrystalMaker can now read from VASP text files that contain Cartesian coordinates, in addition to files with fractional coordinates.
Miscellaneous Changes. Minor changes to CIF file import and generic file handling have been incorporated into this release:
CrystalMaker can now read from CIF files with inline loop headers (all command items placed sequentially on a single line), as opposed to the more conventional (and tidy!) multi-line layout.
CrystalMaker can now recognize generic binary files, with filetype 'BINA'. Such files might include CrystalMaker binary files that have been transferred over a network, resulting in the loss of the native Mac file and creator type information.
VASP 5 Support. This version of CrystalMaker can now read from POSCAR/CONTCAR files in VASP 5 format. Such files optionally include element symbols for the listed atoms, and these will be used by CrystalMaker to assign atom types - instead of having to rely on accompanying INCAR/POTCAR files.
Miscellaneous Changes. Thanks to the positive feedback from various of our users, we have been able to refine CrystalMaker's support for the WIEN2k file format, and provide better matrix output for the Transform Cell command:
When loading a WIEN2k file, CrystalMaker now correctly converts distance units from Bohr to Angstrom units.
WIEN2k Rhombohedral lattice correction. WIEN2k files treat rhombohedral lattices in an unusual manner, specifying hexagonal cell parameters, but giving fractional atomic coordinates relative to a rhombohedral cell. CrystalMaker now converts the unit cell parameters to rhombohedral ones, in order to display the structure correctly.
Recent Files Submenu. CrystalMaker now includes a File > Open Recent submenu, in keeping with many other programs. This submenu provides a quick way of accessing recent files, and is an alternative to the "Files" pane in the Overview window (now renamed "Recent").
By default, the menu lists the 20 most-recent files (the full list can be reviewed in the Overview window). If you wish to change this limit, you can do so using the Terminal (located in Applications/Utilities ). For example, to change the limit to 30 files, enter the command:
defaults write com.crystalmaker.crystalmaker NSRecentDocumentsLimit 30
(CrystalMaker will need to be restarted for the new limits to take effect.)
File Favourites. A new, "Favourites" pane has been added to the Overview window. This allows you to manage, and store, your favourite file references - and will not be modified by the program when new files are opened (as was the case with the former "Files" pane, which served dual use as a repository for favourite files and recently-opened files).
To add a structure to the Favourites pane, do one of the following:
Progressive Undo/Redo. Previous versions of CrystalMaker provided multiple undo levels, each with its own graphical preview, as displayed in the History pane of the Overview window. However, the Undo command toggled between the two most recent states (i.e., the same behaviour used in most Adobe applications).
CrystalMaker for Mac now follows the example of its Windows counterpart (and most modern Mac applications, for that matter), in implementing a progressive Undo command - with a corresponding Redo command. Multiple invocations of the Undo command result in progressively older states being displayed; conversely, repeated use of the Redo command will progressively restore the window state.
Please note that the command-shift-Z keyboard shortcut (which previously triggered the Window > Plot Size command) is now used for the Edit > Redo command.
Elements Toolbar Menu. A new popup menu button has been added to the (default) Window toolbar, which allows quick application of different preset element tables. For example, one can instantly switch to Van-der-Waals radii, or covalent radii, or ionic radii - without the need to display the Edit > Elements window, choose a preset, and click the window's Apply button.
New Default Toolbar. The default window toolbar (which can be restored by right-clicking in the toolbar and choosing the Customize Toolbar command) has been changed as follows:
WIEN2k File Import. CrystalMaker can now auto-detect, and import, ".struct" structures files from WIEN2k: a quasi-commercial an electronic structures calculation package, deveoped at the Technical University of Vienna.
VASP File Import. CrystalMaker can now import structural data files from the quasi-commercial Vienna Ab Initio Structures Package, VASP.
CrystalMaker reads from VASP POSCAR and CONTCAR files, which contain lists of atomic positions within the unit cell (but no atom type data). CrystalMaker will also search for POTCAR and INCAR files in the same directory and, if found, will attempt to assign atom types to the coordinates list, so as to plot a more meaningful structure!
VESTA File Import. As a service to new users migrating from "VESTA" to CrystalMaker, we now support the import of structural data from VESTA text files.
Miscellaneous Changes. This version includes a number of minor changes:
New Tutorial. A new edition of the CrystalMaker Tutorial is included with this release. This has an all-new, single-column layout, designed to be easier to read on a computer screen. Extensive changes have been made throughout the text, with clearer labelling of figures, and including margin notes and standout boxes.
"Lion" Cursor Support. CrystalMaker now supports the display of window-resizing cursors, as displayed at the window edges and corners under Mac OS X 10.7 "Lion".
Miscellaneous Changes. This version includes a number of minor changes:
Thermal Ellipsoid Information. Clicking on an atom with the Info tool's "Info" button prints information about both the site, and - if present - its atomic displacement (thermal) ellipsoid. New data include the actual displacement tensor, plus the lengths and orientations for each of the three principal axes, given in lattice vector form.
Improved Window Menu. The Window menu has a new layout, with additional functionality:
Streamlined Layout. The menu has been streamlined, by moving all of the Toolbar- and Sidebar-related commands into submenus. For example, the Show Toolbar command would now be accessed from the Toolbar > Show Toolbar submenu, and the Show Sidebar command from the Sidebar > Show Sidebar submenu.
Full Screen Control. This menu also includes a new command for switching into, or out of Full Screen mode. This complements the existing Tools palette and window toolbar buttons.
Play Command. Animation of window Views or File favourites is now possible in full-screen mode with palettes hidden, thanks to a new Window > Play menu command. The command changes between Play Views and Play Files, depending on the activate pane of the Overview window (which does not have to be visible, however). Holding down the option key changes the command to Play ... Again, which executes without displaying a dialog, using the last-selected (or default) animation settings.
Miscellaneous Changes. This version also includes miscellaneous improvements in functionality, windowing behaviour, and minor bug fixes:
The unit cell volume and number of atoms in the unit cell are now printed in the Log pane of the Overview window, using the Transform > Formula & Density command.
New windows use the toolbar settings of the previous front window, rather than reverting to default settings.
The Window > Zoom and Window > Minimize commands are now disabled when in Full Screen mode.
Improvements to the network checking have been incorporated in this version, designed to prevent spurious "licence violation error" messages when the program is re-launched following a crash.
Fixed a rare problem with missing atoms caused by a combination of tiny x-coordinates (e.g., 1.0 × 10-17) and the listing of symmetry generators in reverse order (identity operator last).
This is a minor release that fixes a possible problem with the Transform Cell command, in which a valid matrix transformation could have an incorrect lattice type applied, resulting in overlapping atoms.
Cell Transformations. A new Transform > Transform Cell command provides a range of options for specifying lattice transformations, including changing lattice types (e.g., Face-centred to Primitive cell), arbitrary matrix transformations, projecting the unit cell onto an arbitrary lattice plane, as well as the existing Supercell transformations.
A popup menu provides easy shortcuts to commonly used transformations, including changing lattice type, projecting onto (111) and (110) planes, plus various supercell options.
More powerful options can be revealed using the Advanced Options disclosure command:
When the General Transformation mode is selected, users can enter the coefficients of an arbitrary transformation matrix, and have CrystalMaker recalculate the structure. (Note that CrystalMaker checks the matrix to ensure that this is consistent with the lattice periodicity, so that inadvertant changes to the physical structure are avoided.)
The Lattice Plane Projection results in a new unit cell whose x and y axes reside within a user-specified lattice plane (the z-axis is directed out of the plane). This is ideal for working with crystal surfaces, since the number of atomic layers parallel to the surface can easily be defined, in terms of the crystal's z-range.
Moveable Origin. A new Transform > Move Origin command lets you specify a position in the unit cell where you would like the origin to be moved.
You can use this command, in combination with the Selection tools, to move the origin directly to a selected atom, or to the centroid of a multi-atom selection (simply make your selection, choose the command, and click the OK button to proceed).
Full H.264 Support. CrystalMaker now provides full support for the advanced H.264 video compressor. This 'codec' offers a superior combination of output quality and video compression, and is now our recommended choice, ahead of the previous front-runner, the "JPEG 2000" codec.
The H.264 codec includes a range of output parameters; we recommend unchecking the "Key frame" and "Limit data rate" checkboxes, and setting the "Quality" setting to "Medium" or higher. This should result in good-quality output, comparable to the "JPEG 2000" codec in its "Millions/Least Quality" setting, but around half the file size.
DL_POLY History File Import. CrystalMaker can now auto-detect and load "History" files generated by the DL_POLY Molecular Dynamics program. Individual structures - which could be in 'crystal' or 'molecule' format, depending on the Periodic Boundary Condition flag - are loaded in the same window, as separate View thumbnails.
CrystalMaker's unique multi-structure visualization, synchronization and animation allows seamless viewing of the complete refinement trajectory: an ideal way to understand the progress of your modelling calculations!
Faster File Import. CrystalMaker offers a seamless way of rapidly loading multiple data files in one clean sweep: you don't have to use modal import commands, or remember to use proscribed file extensions; instead, just drag-and-drop one or more files into CrystalMaker, and let the program figure out the format(s), using its auto-detection algorithm. In the latest release, we have made this much faster, and the changes will be particularly evident when working with massive data files.
Constrained View Direction. We have redesigned the Set View Direction window, to give the option of specifying a second direction, which should (or whose projection should) be displayed vertically, from the bottom to the top of the screen. This constrains the crystal orientation, and was a feature that various users had requested.
To provide a more elegant, and less intimidating interface, the additional "Vertical Direction" fields are initially hidden. They can be revealed using the new Constrain orientation disclosure control.
Sortable Views. The Overview window's Actions menu includes two new commands to sort View thumbnails in ascending or descending order, according to their titles
This is useful when working with large numbers of views, especially if the views have been loaded, en-masse, from your operating system (which may not necessarily add them in the correct order).
Video Tours. A new Video Tours command has been added to the Help menu. This serves as a link to a new section of our website, where we display a range of video tutorials covering different aspects of the program.
Streamlined User's Guide. The CrystalMaker User's Guide has been streamlined to make it easier to use. The guide now features a one-page table-of-contents, for at-a-glance navigation, plus extensive rewriting and reorganisation of chapters.
Standalone Tutorial. The CrystalMaker Tutorial, which was previously part of the User's Guide, has now been moved to a separate document, and can be accessed via the new Help > Tutorial command.
Improved Support Commands. The Help > Request Technical Support command now assists you by pre-loading important parameters into the support form, including the program name and version, its serial number, plus your operating system name and version.
A new Help > Register CrystalMaker command provides assistance in the registration process, supplying the program name, its serial number, and your operating system to the online registration form.
Miscellaneous Changes. This version includes some additional interface changes, revised atom sphere vector graphics output, and bug fixes for the Molecule-to-Crystal conversion and Full Screen animation:
A "serial number" is now displayed in the "About" screen (CrystalMaker > About CrystalMaker, Mac; Help > About CrystalMaker, Windows). This serial number is unique to your licence, and can be used in place of the licence code, when requesting technical support (please don't forget to specify "Mac" or "Windows" though!).
A new Change Background command has been added to the Graphics pane contextual menu, offering a more direct and intuitive way of changing the background display (instead of having to choose the Model Options command and then navigate to the Background pane).
Minor changes have been made to the ordering of menu items on the Selection menu, and also the Graphics pane contextual menu. These changes should provide a more consistent layout, and better reflect a typical workflow.
The Transform > Supercell command has been removed. The same functionality is now available via the Transform Cell command on the same menu. To access the Supercell options, simply click the Cell Transformation window's Advanced Options disclosure control, and choose the Supercell option in the Transformation type radio group.
More consistent wireframe plotting for "Polyhedral" models. Any sites which have "wireframe" styles now use the same bond colours and styles as in a "Wireframe" model. These can be set using the Bonds pane of the Model Options window.
Workaround for Adobe Illustrator Vector Graphics. We have revised our atom sphere vector output (Mac 'Pict' format) to work around a bug in Adobe Illustrator that caused some spheres to plot as solid dark circles. In the absence of any bug fix from Adobe, we changed our code so that simpler vector output was generated, which Illustrator seems to be able to cope with.
(This was strictly an Adobe Illustrator issue: Other software, including Graphic Converter, Photoshop, Preview and AppleWorks had no difficulty reading the original CrystalMaker vector graphics!)
Improvements to Molecule-Crystal conversion. We have identified a potential problem with earlier versions of the software, where structures have been converted from 'molecule' to 'crystal' mode, but without the correct atom sorting being applied. This could result in memory issues when atoms are deleted. CrystalMaker will now automatically fix these files as they are displayed.
Floating palettes now remain hidden when using the Play command in Full-Screen mode.
Dragging-and-dropping a picture into the Graphics pane no longer causes an "error of type -50" warning.
Fixed a rare issue with the Export > Rotation Movie command which caused VR- instead of linear-video (QuickTime) output. The problem only occurred if the previous video output was in VR mode, but this has now been corrected.
Fixed a bug that caused the List Bonds command to fail when the "Search each selected site" option was checked.
Changes to the Make Polyhedron command. In previous versions of the program there was a potential danger of specifying an over-large polyhedron, where some vertex atoms were related by symmetry to the centroid. The resulting recursion could cause a crash.
The program now warns if another atom exists in the location of the proposed centroid and, if the user opts to continue, a new, dummy atom, is created at the centroid. This avoids problems of recursion, and allows arbitrary-sized polyhedra to be created.
Increased Sophistication for CIF Import. Following the major changes to CIF import introduced in the previous version, we continue to refine our algorithm to cope with extreme subtleties in the data input. For example, the algorithm can now cope with complex strings which have quotes within quotes, such as: 'a dog's life', as well as null strings, or arbitrary-sized strings.
Miscellaneous changes. This version includes some minor bug fixes and performance improvements:
New Import Module for CIF files. Loading of CIF files has been made considerably more robust, thanks to a new algorithm. CrystalMaker can now cope with complex formatting, in which atomic data are divided amongst arbitrary loops, with or without atom labels being present. In addition, error reporting has been strengthened, and the program can recover from minor errors, without defaulting to dummy (and possibibly erroneous) values.
In addition to its robust handling of complex syntax, the new algorithm is also able to cope with truly massive input files (> 100 K atoms).
Improved PDB 'crystal' import. PDB text files that contain (valid) crystal lattice parameters, can now be loaded much faster, thanks to an optimized algorithm. In addition, a bug that could cause the program to crash when loading such files has been fixed.
Miscellaneous changes. This version includes some minor bug fixes and performance improvements:
Animation Presets. The Play Options dialog (accessed from the Play command of Overview Window's Actions menu) has been redesigned, and features a Presets popup menu. Presets cover three common uses of this command: for creating Animations, Slideshows, or showing a sequence of Spinning structures.
Please note that, for reasons of clarity, we have renamed "Kiosk mode" as "Full screen".
Play Button. Animations and slideshows can now be started directly from the Graphics Window's toolbar, using a new Play button. This has the same effect as using the Play command in the Overview Window's Actions menu, and will display the Play Options dialog, letting you animate the window's Views (if the Views pane is active), or your File favourites (if the Files pane is active).
If the Play button is not visible, you can add it to the Toolbar via the Toolbar Customization sheet. Choose Window > Toolbar > Customize (or right-click on the toolbar and choose the Customize command in the contextual menu). When the sheet appears, locate the Play button icon, and drag it onto the toolbar.
Miscellaneous changes. This version includes some minor bug fixes, associated with text file import, and manipulation of Overview thumbnails:
More robust PDB import & error handling. Various enhancements have been made to the PDB import, to handle files with missing atom labels or other invalid data data. In addition, error messages - printed in the Log pane - are now made available following import, so that the user can better assess the scale of any problems.
Improved "Live Rotation" Mode. When using stereo-pair plots, or red/blue stereo, the same structure is always plotted twice, with different orientations for each eye. This resulted in two sets of rotations being transmitted to SingleCrystal, whilst in "Live Rotation Mode", causing simulated diffraction patterns to flicker. This problem has now been addressed, and a single - averaged - orientation is now sent.
Miscellaneous changes. This version includes some minor bug fixes, associated with text file import, window re-drawing, and manipulation of text boxes and other annotation objects:
Improved Animation Movies. Animations, created using View thumbnails, can now be exported as movies with or without looping (regular, or "back-and-forth"), and using full rendering quality.
(Earlier versions of the program allowed basic movie export, using the default rendering mode, and without looping.)
Miscellaneous Changes. This version fixes an issue with some menu items on PowerPC-based systems, and a rare issue with one of the Selection commands:
CIF files from the American Mineralogist Crystal Structures Database now have their database codes displayed in the Notes pane.
Fixed a problem with the Selection > Atoms > Edit Coordinates command which prevented editing if one of the selected atoms happened to be the first atom in the structure. Error reporting has also been improved for this command.
A problem with the Selection > Atoms > Style submenu, on older (PowerPC-based) Macs, has now been resolved. A colour palette was being added to the submenu, resulting in the incorrect behaviour for remaining commands on that menu.
Improved CIF Import. This version fixes various issues arising from import of CIF files with unusual formatting. This includes a problem with reading underscore ("_") characters in undelimited data items.
Miscellaneous Changes. This version includes some minor changes to the graphics, including better optimization during graphics transfer. This should finally resolve a rare issue with pixel trails remaining as a structure is rotated (when using smoothed, "antialiased", lines).
Rotation Movie Export. QuickTime movies of continuously-rotating structures can now be automatically generated, via a new File > Export > Rotation Movie command. You can specify the number of frames and the time to complete one full rotation. Checkboxes allow for looping and "auto play".
Note: if you are using Mac OS X 10.6 "Snow Leopard", you may find that the rather cut-down "QuickTime Player X" ignores the "Auto Play" option. Earlier - more powerful - versions of the QuickTime Player (e.g., version 7) do recognize the Auto Play tag. We hope that this functionality will be restored in future versions of the operating system.
Direct QuickTime VR Movie Export. QuickTime VR object movies can now be exported via a single menu command (File > Export > QTVR Movie), instead of having to use the Video Recorder palette.
Please note that the former File > Export > Video command has now been removed. This command simply displayed the Video Recorder palette, and duplicates the existing Window > Palettes > Video command.
Streamlined QuickTime Movie Generation. CrystalMaker now uses the latest QuickTime system calls to generate cross-platform movies, without the need to create temporary, resource-based files. This means less clutter on your system, and avoids problems when attempting to delete the temporary files.
The new technologies provide a workaround for a system bug which meant that some VR movies were difficult to rotate on "Leopard" and "Snow Leopard".
XYZ File Import/Export. CrystalMaker now supports the ".xyz" file format, with automatic format recognition, allowing seamless drag-and-drop display of data. You can also export in the ".xyz" format, via the File > Export submenu.
Faster Graphics. CrystalMaker now uses highly-optimized graphics transfer to provide faster frame rates when rotating structures with the mouse. For a typical screen, rotating a structure in "mono" is now 25% faster.
Miscellaneous Changes. This version includes numerous subtle enhancements and some bug fixes:
A new edition of theCrystalMaker Setup Guide has been published. This is provided in print form with the full program, and is also available, in PDF format, from the Help menu.
The default frame rate for QuickTime movies has been increased from 6 to 12 frames-per-second.
QuickTime frame rates (fps) and Rotation Movie settings are now saved in the Preferences file.
When exporting a QuickTime VR Movie, or a Rotation Movie, CrystalMaker automatically uses the highest-quality "Full Rendering Mode" graphics.
Database codes are now extracted from AMCSD-derived CIF files, and copied to the Notes pane (and the window title, if appropriate).
Fixed a compiler-related issue that could cause the program to crash when importing text files on Intel Macs. (This problem did not exist on PowerPC machines.)
SHELX files that omit site-occupancy fractions and isotropic temperature factors, can now be read.
Fixed a rare "Singular Matrix" error when calculating new crystals.
A rare, memory-corruption issue, associated with deleting atoms or bonds, has now been resolved. The problem only occurred when a structure had bond specifications with non-zero minimum values.
CIF files with comment ('#') characters in unusual places are now processed correctly. Earlier versions of the program failed to parse CIF files which used the '#' (comment) character in data tags (e.g., the American Mineralogist Crystal Structures Database uses this character as part of its database codes).
Fixed a rare issue in which slow rotations of a structure resulted in trails of unerased pixels left on the screen.
Exported graphics (and video) now show all model elements with the correct degree of transparency. Earlier versions of the software did not explicitly set the alpha channel for exported graphics or video, which could - in rare cases - cause atoms and some lines to appear to be entirely transparent.
Rationalized the diffraction submenu. The Transform > Diffraction Pattern submenu has been split into two separate submenus, one for Powder Diffraction and the other for Single-Crystal Diffraction. This makes it clearer that Live Rotation Mode applies only to single-crystal diffraction - and gives us more scope to add future commands for each technique.
Fixed a rare problem reading from old binary files on Intel systems. CrystalMaker binary files which had been saved on a PowerPC machine, then copied to an Intel machine, without the correct file extensions, and with no file-type/creator codes, could not be read.
Whilst we do recommend that users remember to apply the correct file extensions (increasingly important, now that "Snow Leopard" relies almost exclusively on file extensions), we also recognize that with extensive libraries of older files, this may not always be practicable. We have therefore made changes to ensure that CrystalMaker can now quickly inspect such files - and correctly determine their readability.
Modernized Code. This version includes more "under-the-hood" enhancements that improve the performance in a number of areas, including:
Optimized the File > Open dialog, to make it faster to filter acceptable file types.
Modernized cursor display. CrystalMaker now uses up-to-date "Cocoa" system calls to display cursors, in place of the traditional, resource-based scheme.
"Drag-and-drop" support has been rewritten to take advantage of changes in how the system processes such events.
Improved Synchronization. The Synchronize command now takes into account the coordinates of a structure's plot centre. This will be applied to the other structures being synchronized, if the Range option has been selected.
(In earlier versions of the program, synchronizing the plot range resulted in structures being auto-centred within the Graphics pane. Whilst this worked well for many animation sequences, in some cases, crystal structures with relatively-small numbers of atoms might appear to "wobble", as the geometric centre shifted from frame-to-frame, owing to some atoms moving into or out of the plot range.)
Improved Drag-and-Drop. File aliases can now be dropped into the Graphics pane, for successful loading of "crystal", text and graphics files. A rare problem in which invisible "dot" files could be dropped, has now been resolved.
Refinements to CIF file loading. CIF files containing empty strings for key data, such as atomic coordinates, can now be processed. Any sites with missing data are removed, and a warning message appears in the Log pane of the Overview window.
New "Visible Coordination" File Export Option. You can use the File > Export > Visible Coordination command to generate a text file that summarizes the connectivity of the displayed structure.
The "Visible Coordination" file lists each atom that is visible on screen. After each atom is a list of the bonded neighbours (if any) and their distances, and the resulting coordination groups are separated by blank lines.
New "Crystal Coordination" File Export Option. The Export > Crystal Coordination command is designed to provide an accurate summary of the coordination states in an ideal crystal lattice.
The resulting "Crystal Coordination" file lists every atom in a single unit cell—regardless of whether or not this atom is visible on screen. If global bond specifications have been defined, then CrystalMaker will use these to generate a list of nearest neighbours for each atom. The resulting coordination groups are separated by blank lines.
Please note that, unlike the Visible Coordination command, the Crystal Coordination command uses crystal symmetry to provide a complete bond listing for the unit cell, regardless of the current plot range and/or atom site visibilities.
Miscellaneous Changes. This version includes various "under the hood" changes, plus a few bug fixes:
Arrow-Key Structure Rotation. Structures can now be rotated using the arrow keys on your keyboard, if the Hand (Rotate) tool is active. This should make structure manipulation easier for those using the new, compact Apple keyboard - or a laptop keyboard.
The left and right arrows rotate a structure about a vertical axis, which runs from the bottom to the top of the screen (the screen Y axis). The up and down arrows rotate about a horizontal axis (left to right) - the screen X axis. Hold down the shift key to rotate about an axis out of the screen: the up and left arrows rotate the structure left (i.e., anticlockwise); the down and right arrows rotate the structure "right" (i.e., clockwise).
More Flexible MOLfile Import. Criteria for MOLfile validation have been relaxed somewhat, so as to allow the import of files written by some third-party software which didn't include all parameters on the Counts and Atoms lines.
Updated User's Guide. The full edition of the CrystalMaker User's Guide (available using the Help > CrystalMaker User's Guide command) now includes detailed advice on QuickTime™ compressors (codecs) and has been updated to include recent changes to the program.
Miscellaneous Changes. This version includes various "under the hood" changes, plus a few bug fixes:
High-Contrast Red/Blue Stereo. CrystalMaker 8.2 provides even more spectacular 3D imaging, using a new high-contrast rendering model to give crisper, and even more tangible stereo graphics in the "Greyscale" rendering mode.
Colour Red/Blue Stereo. Coloured 3D stereo models can now be viewed "out-of-the-screen" using red/blue spectacles. This is in addition to the bold greyscale and black-and-white red/blue stereo options; simply choose Stereo Red/Blue from the Rendering menu, and leave the colour mode set to Colour.
Please note that when using Red/Blue Colour Stereo, you may wish to edit some of the colours in your plot - specifically, colours with hues close to pure red or pure cyan (since these are cut out by the right-, and left- lenses, respectively). For best results, choose colours with hues that are intermediate between red and cyan, i.e., the colour ranges orange-green and indigo-blue.
Accelerated Background Graphics. CrystalMaker 8.2 uses a highly-efficient mechanism for combining high-resolution background graphics (pictures or gradients) with your structural model, allowing faster manipulation than ever before.
You can drag-and-drop a high-resolution graphics file (in any supported format, including PNG, TIFF and JPEG) into the graphics pane, for use as a background picture. In previous versions of the program, performance could suffer if the background picture was very large. CrystalMaker 8.2 provides performance that is orders of magnitude faster.
Comprehensive New Background Gradients. CrystalMaker 8.2 provides extensive new gradient shading options. Two brand new options - radial and reflected - plus new angle and scaling parameters, give professional-level control to your model display.
The Background pane of the Model Options window now includes slider controls for adjusting gradient angle and scale - options which are available for each of the four new gradient types: Linear, Reflected, Radial and Diamond.
Note that the old "Up" and "Down" options are now replaced by the "Linear" option, which gives you full control over the gradient direction and scale. The old "inwards" and "outwards" options are replaced by the new "Diamond" option, and correspond to a 45° rotation.
Gradients can be scaled and rotated, using the slider controls provided in the Background pane of the Model Options window. In addition, gradient starting- and ending- colours can be chosen independently of the "plain" background colour; the gradient colours can be switched, using a handy new "flip" icon.
Live Model and Rendering Controls. Starting with CrystalMaker 8.2, you can now adjust many Model and Rendering Options settings in real time - including reflectance settings, illumination direction, background shading and much more.
Simply hold down the option/alt key as you click a button or adjust a slider control in the Model Options or Rendering Options windows.
Miscellaneous Changes. This version includes various "under the hood" changes, plus a few bug fixes:
Extended Density Calculations. The Calculate Formula and Density command (Transform menu) now includes additional data. Density is now given in both conventional kg/m3 units and traditional g/cm3 units. In addition, the number of atoms per unit volume is calculated and printed in the Log pane of the Overview window.
More Detailed Summary File. The File > Export > Bond Data command now generates a more detailed output file. This includes site multiplicities (numbers of specific sites per unit cell), as well as higher precision for density (kg/m3 and g/cm3) plus number density.
Improved Network Checking. The program's network checking procedure (which compares usage with the licensed limit) has been strengthened, and now correctly takes account of the software platform being used.
Miscellaneous Changes. This version includes various "under the hood" changes, plus a few bug fixes:
Improved Site Merging. When reading from CIF or SHELX files that contain multiple site definitions (representing substitutional disorder), occupants are now sorted correctly, so that sites can be identified by their major occupants.
Expanded User's Guide. The PDF User's Guide has been updated and thoroughly revised. It now includes an new introduction, with installation details, a dedicated Interface Overview chapter plus an expanded index.
Miscellaneous Changes. This version includes various "under the hood" changes, plus a few bug fixes:
Faster loading of massive CIF files. CIF files containing massive structures (e.g., > 100,000 atoms) can now be loaded easily. The speed of loading for larger structures is improved by several orders of magnitude.
Improved Unit Cell Lines. The unit cell frame, when depicted using dashed lines, is now correctly scaled for changing output size/resolution. In addition, changing the line width now causes the length of the dashes to be scaled in proportion, giving a more consistent appearance.
Error Reporting for the Place Molecule command. The File > Place Molecule command now provides better error reporting when, for example, attempting to use an older file whose format is not supported, or when file errors are encountered.
Improved Preferences. Choosing to reapply saved preferences now correctly positions the Graphics window - taking into account whether or not the toolbar is visible. In addition, any recently saved Model or Rendering Options are correctly applied, and the Files pane is correctly loaded. When reverting to "Factory Settings", the Files pane is cleared.
Improved SHELX Support. CrystalMaker now handles site occupancy data correctly for special cases where the occupancy data are constrained or refined. CrystalMaker reads free variables (FVAR cards) from the SHELX file, and uses these to decode site occupancy factors from the supplied data (which may include large negative values).
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Assemble Views by Dragging-and-Dropping Files. Window views can now be created simply by dragging-and-dropping any CrystalMaker- or text file directly into the Views pane.
This provides a quick, easy - and intuitive - way to assemble the frames of an animation or movie. Just drag-and-drop the files you need directly into a window's Views pane. Each file is loaded into the Graphics window and a corresponding thumbnail (or set of thumbnails for a multi-structure file) appears in the Views pane.
(You can also add multiple Views to the Views pane by clicking the window's Add (+) button, and using the resulting File dialog to specify your files.
Window views can then be synchronized, rearranged, updated or deleted, before being displayed as an animation (Actions > Play) or exported to a movie (Actions > Save as Movie).
Torsion Angle Signing. Torsion angles - as measured using the Torsion Angle tool, from the Tools palette - are now signed.
The torsion angle between four atoms A-B-C-D is the angle by which the vector A-B must be rotated in order to eclipse the vector C-D when viewed along the vector B-C. Torsion angles are generally expressed in the range −180° to +180°. According to convention, a positive sign denotes a clockwise rotation (of the vector A-B), and a negative sign denotes an anti-clockwise rotation.
Easier Data Browser Editing. Data cells can now be edited by double-clicking their contents. This applies to all Data Browsers, as used by the Edit > Structure, Bonding and Elements commands, as well as the Site Browser.
Authentication Check for Multi-User Licences. Multi-user licences can now be installed from accounts that do not have administrator privileges. The user will now be prompted to enter an administrator password which, if successful, allows the program to complete the appropriate "all users" installation.
Improved HTML Output. Web page output has been greatly improved. Oversize graphics are now scaled down to fit within the page size. Data tables are more attractive and now contain far more information, including:
Expanded Documentation. The CrystalMaker User's Guide has been revised, with updated and expanded coverage of window Views (Chapter 1: Getting Starting) and the resulting movie generation (Chapter 9: Making Movies). Online Help files have also been updated for this release.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Powerful Atom Info Tool. This tool now provides much more detailed information about the clicked site. Clicking the small "i" button in the Atom Info "tool tag", now results in the Log pane of the Overview window being made visible, with the following data printed:
Enhanced Optimize Range Commands. The Hide/Repair Molecular Fragments commands are now significantly faster - especially for larger structures. In addition, if these commands fail (i.e., tje structure is not a molecular crystal), then the previously-displayed structure is correctly restored.
Customizable Printer Resolution Output. CrystalMaker supports a new Leopard system feature, allowing the program to print at user-defined resolutions for certain supported devices.
The resolutions are defined in the Print Features section of the standard Print sheet (e.g., some PostScript printers may give a choice of 600 or 1200 dpi output).
Improved ATOMS File Support. Spacegroup symbols and origin choices are now read from text files in the ATOMS format, thereby avoiding problems with possible missing symmetry generators in such files. Bond and polyhedral specifications are now merged, to ensure more consistent results in CrystalMaker.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Extended CIF Output. Site occupancy data and atomic displacement parameters ("thermal ellipsoids") are now exported to the CIF format.
More Powerful Spacegroup Recognition.
Spacegroup symbols that use parentheses
to designate subscripts (International
notation) can now be recognized. For example,
P 2(1)2(1)2 for
P 21 21 2.
This should mean that CIF and other file formats are
easier to load.
Improved Vector PICT Export. A workaround to a long-standing system issue with vector graphics, has been introduced. This avoids an occasional issue with varying line thicknesses in exported vector graphics.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
ATOMS File Support. CrystalMaker can now read text files produced by the old "ATOMS" program from Shape Software. CrystalMaker handles the more recent "version 4" and "version 5" formats, extracting the essential crystallographic data, plus atom colours and radii, bonding and polyhedra.
Popup Toolbar Buttons. Popup menus have been added to the Model Options, Rendering Options and Overview window toolbar buttons. These menus allow direct access to specific panes within the relevant windows - so for instance, one can now quickly set a window's background settings by choosing Backround from the Model Options popup menu.
PDB Connectivity Data. A problem with "mangled" bond data in exported PDB files has now been resolved. When exporting a PDB file, all visible sites are listed in the output file, together with their serial numbers and full connectivity information.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Loop Back and Forth. The Overview Play command now gives a choice of looping, either unidirectional ("left-to-right") or bidirectional ("back-and-forth").
Open Multiple Files as Separate Views. Opening multiple files into the same Graphics window now results in each structure being opened, as a separate view, in the same window (this is analogous to opening a multi-structure file).
The multiple files should be loaded simultaneously, in one of the following two ways, either:
or:
Please note that opening a single-structure file does not automatically add a view to the Views pane.
Synchronize Again Toolbar Option. Users can now synchronize more quickly, suppressing the Synchronize Options sheet, and using the last-specified settings. Simply hold down the option key whilst pressing the Synchronize toolbar button.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Live rotation link with SingleCrystal. CrystalMaker and SingleCrystal can now be linked, so that rotating a structure in CrystalMaker causes the corresponding diffraction pattern to rotate in SingleCrystal (and vice versa).
To initiate the live link, enable CrystalMaker's Transform > Diffraction Pattern > Live Rotation option, then simulate a diffraction pattern directly from CrystalMaker, using the Transform > Diffraction Pattern > Single Crystal command. Your current structure is now linked with a new window in SingleCrystal.
To stop the live link, simply uncheck the Live Rotation menu command.
Porosity Calculation. The amount of free space in a crystal can now be calculated, thanks to the new Transform > Calculate Porosity command.
Note: This command uses the currently-set sphere radii for its calculation. Users may wish to switch to Van-der-Waals radii for the most appropriate results.
New "Fit Plane Through Points" algorithm. A new, two-stage algorithm is now used for fitting a lattice plane to a set of selected atoms. The algorithm uses a more-accurate starting model, with a subsequent least-squares refinement process, resulting in more precise and reproducible results, that are largely independent of the starting orientation.
Molfile and SDfile import. Elsevier-MDL "Molfile" and "SDfile" formats are now auto-detected and loaded by CrystalMaker. As with other multi-structure formats (e.g., PDB and CIF), the individual structures saved in an SDfile are loaded into the same window, and represented by thumbnails in the Views pane.
Faster loading of text files. CrystalMaker now uses a two-stage file-type detection process, resulting in much faster loading of text files that have recognized file extensions. This improvement is most noticeable with larger, multi-structure files, such as PDB, CIF and SDfile formats.
(CrystalMaker can still auto-detect and load file formats that do not have file extensions, or which have non-standard extensions.)
More Flexible Views. Existing CrystalMaker binary files can now be dragged-and-dropped into the Views pane of the Overview window. This should facilitate the building of movies or animations, by allowing previously-saved files to be easily added (en masse) to an existing project.
Colour Shortcut Menus. Colour buttons, used for setting the background colour(s), unit cell and axial vector colours, surface colour, lattice plane colour, and so on, now include popup menus with colour shortcuts.
View Direction Menu Button. The window toolbar's View button now has a popup menu, allowing you to quickly set the orientation along commonly-used directions (e.g., a, b, c, a*, b*, c*, etc.).
Live Element Table Switching. A new Live Update checkbox has been added to the Element Editor window (Edit > Elements), letting users browse different element tables (e.g., via the window's popup menu), and have their structure be immediately replotted.
Lattice Plane Support for Angle & View Direction windows. The orientation of the last-displayed lattice plane can now be recalled in the View Direction or Calculate Angle windows. Both of these windows now feature popup menus, to the right of the orientation fields, which include the lattice plane normal.
This new feature streamlines the process of calculating angles between planes, for example, the angle between two benzene rings in a molecular crystal:
Miscellaneous Changes. This version includes a large number of additional changes, the most-important of which are summarized below:
Redesigned Lattice Plane Sheet. The Lattice Plane sheet (Transform > Lattice Plane > Edit) has been redesigned. The sheet no longer has a show checkbox; instead, a new show/hide item has been added to the Lattice Plane submenu.
Mouse-Wheel Support for Atom and Bond Lists. The Atom Options and Bond Options lists in the Model Options window can now be scrolled using the mouse wheel.
Improved Synchronize Command. The Synchronize command has been extended, to allow for cases where structures have different numbers of atom types/styles. The option to synchronize bond specifications now works correctly.
Chemical MIME Support. Chemical MIME format descriptors have been added for PDB, CIF, MOL and MacMolecule file formats.
Fixed "Unsorted Structure" Warning. Some CrystalMaker binary files (including our Periodic Tables examples) gave spurious "unsorted structure" warnings when loaded. Such structures are now correctly processed and, after re-saving them, can be reloaded without warnings.
Fixed Old-Format Plane/Vector Calculation. Old-format (CrystalMaker 2-4) binary files could result in errors when attempting to convert lattice plane normals to lattice vectors, or vice versa. This issue has now been corrected.
Improved Drag-and-drop. Dropped structures are now opened in the correct window, which is not necessarily the frontmost Graphics window.
Reveal in Finder command. It is now possible to locate the source file for an Overview File thumbnail, and have this selected in the Finder. Simply control- or right-click on a File thumbnail, then choose the new Reveal in Finder command from the contextual menu. (You can also use the contextual menu to show the file path, select the file path submenu, and have the source file displayed in the Finder.)
Multi-structure Error Recovery. When loading a multi-structure CIF or PDB file, the program no longer abandons import when an error is found; instead the program attempts to skip the erroneous data set and moves on to the next set.
Faster Zapper! The Zapper Tool is now much more responsive: the "pow" sound plays at the same time as the "zap" animation (which is slightly faster).
Improved Update Version. In order to prevent confusion about installing the update version, CrystalMaker will now refuse to run from a disc image. Instead, it will display an alert instructing users to copy the application from the disc image to their hard disc.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Enhanced CIF support. Error values for cell parameters and fractional coordinates can now be read from CIF files. These data are used in the program's error propagation, when measuring interatomic distances on screen, via the Transform > List Bonds command, or in the File > Export > Bond Data command.
Easier scaling of Overview thumbnails. Thumbnails displayed in the Views, History or Files panes of the Overview window can now be scaled by holding the command key down and moving the mouse wheel up or down (i.e., the same method that is used for scaling a structure in the Graphics pane).
Improved Bond Data Export for Molecules. The File > Export > Bond Data command now gives more specific information for structures in "molecule" mode. Atom numbers, labels and orthogonal coordinates are summarised, followed by the standard listing of bond distances and angles for each atom.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Faster Overview Play command. Rotation of structures via the Play command (Overview window's Actions menu) is now much faster. When the Rotate each structure option is specified, the program now uses your Rendering > Fast Rotation Mode or Full Rendering Mode settings.
Customizable Spell Checking. The Check Spelling As You Type option is now off by default. This option can be enabled via the Edit > Spelling submenu, or by using the Notes pane contextual menu. Your spell checking choice is now saved in the program's preferences file.
Improvements to Overview Log. Output to the Log is now retained correctly, even if the Overview Window was initially hidden when the output was generated.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Workaround for Tabbing Bug on "Tiger". We have introduced a workaround for a potential problem when tabbing in a data browser (e.g., Edit Crystal, Edit Bonding or Edit Elements). Changes made to support tabbing under "Leopard" could occasionally result in the program crashing under "Tiger".
Native "Tiger" and "Leopard" Support. CrystalMaker 8.0 for Mac is designed to run natively on the latest versions of Mac OS X, 10.4 "Tiger" and 10.5 "Leopard". Windows, sheets and data browsers have been updated to take advantage of new operating system capabilities. This application is provided as a universal binary, delivering native performance on both PowerPC and Intel processors.
Spotlight. Find files by chemical composition, density, cell parameters, volume, spacegroup, crystal system or notes. You can customize your Finder-based search criteria to include multiple requests, such as all files containing "Ca" and "O" with densities between 1500 and 2000 kg/m3.
QuickLook. (Mac Leopard/Snow Leopard) Instantly preview the contents of your CrystalMaker binary files (*).
CoverFlow & File Previews. (Leopard/Snow Leopard) Browse through high-resolution previews of your CrystalMaker binary files in the Finder's CoverFlow mode. View preview icons in other Finder modes (*).
Edit Thermal Ellipsoid Data. Isotropic and/or anisotropic displacement parameters can now be edited using a completely-revised Edit Crystal window. Users can customize the data display, with the option of basic (coordinates-only) through to advanced (all data) view settings.
Supercells. Multiple unit cells can be merged into a single unit cell, thanks to the new Transform > Supercell command. This is especially useful when attempting to generate input for computer simulation studies.
Molecule-to-Crystal Command. Convert aperiodic molecular data into periodic, crystallographic data. Ideal for working with computer simulations where tiling is required, or for simulating diffraction patterns from molecular data.
New Monoclinic Spacegroups. Unconventional monoclinic spacegroups are now recognized, and supported, by the Edit Crystal window. These include 29 new spacegroups with their unique axes parallel to a, as well as spacegroups with unique axes parallel to b and c.
"Hidden" Orthorhombic Spacegroups. All known settings for orthorhombic spacegroups have been added to CrystalMaker. These include spacegroups which are not listed in the International Tables for Crystallography because they have the same symbols as other settings, albeit with slightly-different symmetry operators (GEPs).
An example is spacegroup 17, P 2 2 21 which is listed as having three unique settings (position of the screw diad) out of a maximum of six possible axial settings (abc, acb, bac, cab, bca, cba). However, closer inspection reveals that spacegroups with the same symbol, but different axial settings, are not quite identical, e.g.,
axial setting abc yields spacegroup P 2 2 21 with origin at 2 1 21
axial setting bac yields spacegroup P 2 2 21 with origin at 1 2 21
These unique settings are now listed as different "origin choices" for the relevant spacegroup symbols.
List Atom Types Command. A new command to summarize the number of atoms currently displayed on the screen, and the number of different element types. The chemical formula for the current display (c.f., the ideal formula for an infinite crystal) can also be shown.
Automatic Positioning & Scaling of Atom Labels. Atom labels can now be automatically positioned so as to minimize the chance of overlap. This is a new option (checkbox) in the Labels pane of the Model Options window (which also gives the option of static label positions). Label positioning is further enhanced by using font metrics to better vertically-adjust the label.
Another new Atom Label option is to have labels automatically rescaled as a structure is zoomed. This can be useful when you need to start with an extended structure (e.g., a molecular crystal) and then cut away much of the structure to reveal a sub unit. The atom label size automatically adjusts as the scale changes, so that labels remain correctly proportioned relative to atom spheres.
Labels-to-Textboxes Command. As an alternative to relying on automatic label positioning, you can opt to convert selected atom labels into textboxes. These can then be edited and moved freely - ideal for final output.
Thermal Ellipsoid Sphere Override. One of our most frequent requests was the possibility of turning off thermal ellipsoid display for specific sites in a structure, and to plot those sites (generally H atoms) as small spheres.
The Atoms pane of the Model Options window now includes thermal ellipsoid checkboxes in its scrolling list. Turning off a checkbox causes that site to be plotted as a sphere. The sphere radius can be customized using the new Thermal Ellipsoids Sphere Radius text edit field.
Customize Ball-and-Stick Sizes. We have opened up the program to allow control over the relative radii of ball-and-stick spheres (compared to space-filling spheres), and the minimum radius used to plot ball-and-stick spheres. These settings can be edited via new text fields in the Atoms pane of the Model Options window.
Intelligent Auto Scaling. CrystalMaker features a new display mode which adapts to changing plot size by automatically scaling the structure; you no longer have to switch into or out of "Auto Scale" mode (although there is a command to scale the structure to fit within the current plot size). The new scheme makes it easier to switch into, and out of, full-screen or kiosk mode, without having to repeatedly zoom in or out.
GSAS File Import.
GSAS (".exp") files can now be
imported. The file format is auto-detected,
so in most cases you can use the File > Open
command with these files. As with other
file formats, CrystalMaker is strict about
enforcing file formatting rules.
PDB Crystal Import.
PDB files that contain the requisite
crystallographic data (e.g.,
CRYST1 card) can now be loaded
as crystals, giving full access to the
program's features including display of
thermal ellipsoids and simulation of
diffraction properties (via SingleCrystal or
CrystalDiffract).
Note: The original PDB "molecule" view is preserved, following crystal import. Temperature factors are imported following successful validation.
Improved PDB File Handling. Multi-structure PDB files are now loaded as separate views in the same Window, thereby allowing easy comparison and animation.
Loading of large PDB files is now considerably faster than in previous versions.
When exporting a structure in PDB format,
the connectivity information is now saved, using
CONECT cards. Any crystallographic data
are exported in REMARK fields.
Improved CIF File Import. Multi-structure CIF files are now loaded as separate views in the same Window, thereby allowing easy comparison and animation.
Structures loaded from the same CIF file
(into different window views) are named
using the CIF data_ block descriptors.
Where a CIF file contains both a spacegroup symbol and a spacegroup number, we give priority to the symbol, as this generally gives a more detailed summary of the structure's symmetry.
Synchronize Windows and Views. Perhaps the most-powerful and useful command ever! Choose your master view or window, execute the Window > Synchronize command and use the sheet to specify which options you'd like to synchronize. Finally, press the OK button to update all other views or windows.
Multi-Structure Animation. Effortlessly browse through huge numbers of structures saved in multi-structure CIF or PDB files, compare adjacent "frames" with a press of the arrow key, and save an animation with a single menu command. This is a great way to analyse structural changes and phase transitions!
Use the new Synchronize command to synchronize all of your Window's views. This way you can set your model type, bonding, colours and plot range for one structure, and have your changes automatically applied to all other structures.
Rename and rearrange the subviews, then use the Overview Window's Actions menu to automatically save the views as an animation, in QuickTime movie format.
File Favourites. With the new Overview Window you can organise unlimited numbers of recent or favourite files. Simply drag-and-drop files (text or binary) or folders (e.g., your entire structures library) into the Files pane of the Overview window, and thumbnails/icons will be automatically generated. Drag thumbnails to rearrange them, then click to load the structure.
Slideshow/Kiosk Mode. The Overview Window's Actions menu has a new Play command, letting you display animated slideshows for all your favourite files or window views. You have the option of rotating each structure, looping the animation or slideshow and using "Kiosk Mode" in which all user interface elements are hidden: great for presentations or demonstrations.
Full-Screen Working. Focus on your work with the new Full Screen mode. Your structure is automatically zoomed to fill the screen and extraneous clutter hidden. Automatic menu bar and dock hiding is enabled, and you can summon up the appropriate palette windows to access the full range of tools, as needed. To cancel Full Screen mode, simply click the escape key.
Cycle Through Windows. A new Window menu command lets you cycle forwards or backwards through multiple windows. This is particularly effective in full-screen mode.
Fast View Selection.. The Set View Direction sheet/dialog includes four new buttons for immediate access to common view directions:
a, b, c, [111]
Clicking one of these buttons causes the orientation to be applied and the sheet/dialog immediately hidden. Holding down the option/alt key gives access to a further four directions:
N(100), N(010), N(001), N(111)
Spell Checking. The notes pane of the Graphics Window now supports automatic spell checking. To enable or disable this, use the pane's contextual menu, or use the Edit > Spelling submenu.
Streamlined Overview. The Overview Window has been completely redesigned. It now provides drag-and-drop access to custom window views, favourite files and undo states. A "Log" pane replaces the previous Output Window, thereby reducing window clutter. Thumbnails can now be dynamically resized, using a slider control, and custom window views (snapshots) can be updated using a new "Replace with Current View" contextual menu command.
Window Toolbar. An (optional) window toolbar can now be displayed, in addition to the floating tools palette. The two are designed to complement, not replace each other (though the Window toolbar can be customized to replicate much of the Tool Palette functionality).
The Window toolbar is primarily aimed at providing handy shortcuts to commonly-used features, such as showing or hiding the window notes, sidebar or grid, setting view direction and range, and synchronizing windows/views.
Three default toolbar layouts are provided: Standard, Extended and Viewer. These can be selected via the Toolbar submenu on the Window menu. Users can also customize the toolbar in the usual way (control- or right-click in the toolbar and choose the Customize command), with a choice of over 40 commands.
Window Sidebar. The Graphics Window can now display a sidebar containing both a Site Browser and a Notes pane (earlier versions of the program had just a Notes pane). The sidebar can be customized via the Sidebar submenu of the Window menu, or by clicking the Sites or Notes buttons in the Window toolbar. To adjust the relative size of the two panes, click and drag the horizontal divider; double-click the divider to hide the Notes pane (or to show the Site Browser if that pane is hidden).
If you are working with a large number of open windows, you may prefer instead to hide the Sidebar and display a single, floating Site Browser palette (Window > Palettes > Site Browser). The floating Site Browser palette is also available when working in full screen mode (when the window sidebar is hidden).
Fonts Panel. The Notes pane of the Graphics window now supports the Mac OS X Font Panel. This panel replaces the Text menu of the previous version). To display the Font Panel, use the Notes pane's contextual menu, or choose the Edit > Font submenu.
Miscellaneous Features. This version includes a multitude of "under-the-hood" improvements, including:
Faster Import of Text Files. Improvements in the Status Window's progress display have led to dramatic speed increases when importing structural data from a text file!
Plot Range Options. The Plot Range window has been made more powerful with buttons to display a single unit cell's contents and to add integral numbers of unit cells along specific axes.
Discard Symmetry Command. This command is useful when preparing input for computer simulation work, transforming your crystal's spacegroup symmetry to 'P 1', whilst retaining the existing cell contents (i.e., the asymmetric unit is extended to include the full cell contents).
Multi-Row Browser Selection. The Edit Crystal, Molecule and Elements data browsers now support drag-selection of multiple rows. The selected rows can then be edited collectively, or deleted with a single button click.
New Ruler & Grid. The Graphics window has a new ruler with a more intelligent system of tick mark labels. The grid display is now centred horizontally and vertically.
Improved Site Browser Icons. Atom icons displayed in the site browser now use shadows. Hidden sites are shown as rings and sites with small spheres or wireframe display use smoothed discs.
New Tool Icons. The Tools Palette sports new, colour, tool icons.
New About Box. The program's About window has a new, uncluttered look, whilst providing access to more information about the current software licence, including the option of displaying the software licence agreement in a separate window.
Improved Listing of General Equivalent Positions. General equivalent positions for all but a handful of (cubic) spacegroups are now displayed in the same order as that used by the International Tables for Crystallography. (This feature is added for the convenience of users; it does not affect the calculation of atomic positions.)
Resizable Spacegroups Browser. The Spacegroups Browser (formerly the "Symmetry Browser Window") is now resizable and provides more detailed information such as cell/origin choices for unconventional spacegroup settings.
Workspaces. A number of preset window layouts can now be accessed via the Window > Workspace menu.
Live Window Resizing. Structures can now be replotted in real time as a window is resized (this depends on your machine speed; slower machines and/or larger structures may not provide this feature).
Access to Online Crystal Structures. A new Help > Find a Crystal Structure command takes you directly to the CrystalMaker Crystal Search web page, allowing you access to some of the world's most comprehensive crystal structures databases.
Handy User's Guide. The full edition of the CrystalMaker's User's Guide is now available directly from the Help menu. The guide is saved as a PDF document, which is embedded within the application bundle.
New Selection Commands. New commands to select textboxes, vectors or all objects have been added to the Select submenu of the Selection menu.
Network Licence Checking. Multi-user licences now use active licence checking technology. Users upgrading their licences (e.g., increasing the user limit of a group licence) can now use the new CrystalMaker > Reset Licence command.