These notes refer to a legacy product that is no longer supported. Please order your CrystalMaker 9 for OS X upgrade, and look forward to a new era of advanced chemical & materials modelling - plus our usual service and support!
Miscellaneous Installer Improvements. This version includes improvements to the installation for new and update versions.
A problem which caused an invalid licence code error when running the Full Installer on existing installations has been fixed.
Information regarding the Uninstaller is now correctly written to the Registry when a reboot is required following installation or updating.
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.
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:
Invalid values entered into controls in tabbed panes (such as the Atoms pane of the Model Options window) are now validated when the Apply button is clicked or when the window becomes inactive due to window or application switching.
The Site Occupancies column is now displayed only when site coordinates are displayed in the Edit Structures window. Also, the temperature factor columns have been adjusted to fit better in the window.
Prevented a potential hang which could occur if Log pane output was generated during playback from the Overview window.
Fixed a rare issue with loading Cambridge Structures Database FDAT files, for certain hexagonal or cubic crystals. Some translation operators could be omitted.
Thermal ellipsoids defined in the (little-used) βij notation now have their off-diagonal elements correctly sized.
Improved File Association behaviour on Windows XP. When installing on Windows XP systems, the user will no longer have to deal with the "Run As" dialog and risk seeing spurious crash alerts.
Note: When performing the Edit > File Associations command on Windows XP systems, the "Run As" dialog will be displayed by the operating system. You must un-check (clear) the "Protect my computer and data from unauthorized program activity" checkbox, or file associations will not be set and a spurious "application crashed" alert will appear.
Fixed incorrect atom selection in Define Cluster command. A problem which could sometimes lead to the wrong site being selected as the centroid of a cluster when using the Transform > Define Cluster command has been corrected. As a result, sites listed in the pop-up menus in the Define Cluster and Bond Search dialog boxes and in the Atoms pane of the Model Options window are also now sorted correctly (i.e., in the same order as displayed in the Site Browser).
Improved VASP File Import. VASP POSCAR and CONTCAR files containing comments following numeric lattice data are now recognised.
Improved Annotation Tool. Fixed a problem which could lead to a crash when an annotation item was selected using the Annotation tool (rather than the Arrow tool).
More Robust Installation Procedure. Fixed a potential problem which could prevent proper licensing during installation.
Fixed an intermittent problem with the application freezing. This release fixes a problem in which the application could freeze when warnings were issued on file input and the Log pane was the active Overview Window pane.
Improved Video Recorder Palette. The Video Palette buttons have an improved, clearer appearance, making it easier to visually determine the status of the recording. If the Video palette is in QTVR recording mode and the AVI mode button is clicked, the Stop|Pause|Record buttons are now restored to their correct state for linear video recording.
Miscellaneous Fixes and Enhancements. Improvements have been made to file loading, the Lattice Plane dialog, and diffraction pattern synchronization:
Choosing Transform > Single-Crystal Diffraction > Link with Existing Pattern when there is already an active synchronization session with the frontmost helper app window no longer causes the app to freeze and misbehave.
The Lattice Plane dialog now displays up to 3 decimal places for non-integer Miller indices.
When loading multiple files into an Overview Window pane, the pane will remain visible until all the files have loaded (before switching to the Log pane to show any associated output).
Data files (e.g., CIF or STRUPLO files) with .txt and .text extensions can now be dragged and dropped into the application.
Signed Code. All CrystalMaker Windows products are now code-signed using a certificate from DigiCert, giving you confidence that the software you are installing and running on your computer is authentic and safe. Code signing also makes installation easier - especially on Windows 8.
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.
Miscellaneous Fixes and Enhancements. This release contains a few improvements made since the 2.6.4 release:
Fixed problem which could cause a crash when performing cell transformations when sites are too close to unit cell boundaries.
Improved identification of resulting lattice type when performing cell transformations.
File Association Support. The Installer and Updater now allow the user to fine-tune file associations. Choosing the File Association component during installation or update brings up the File Associations dialog, which allows you to specify which document types are opened by default by CrystalMaker.
You can also do this from within the application by choosing Edit > File Associations.
Show Molecular Cell Tool Button. The default toolbar now includes a handy shortcut for visualising 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 visualising 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 > Optimise Range submenu.)
Support for DL_POLY version 4 HISTORY files. CrystalMaker now supports importing of DL_POLY_4 HISTORY files, as well as the older DL_POLY_2. The file version is detected automatically. Note that it is may be necessary to explicitly choose the File > Import > DL_POLY command to import a HISTORY file.
Scientific Notation Supported in CIF Files. CrystalMaker can now read data from CIF files which use scientific notation (e.g., 1.5E+2) for floating-point numbers. Whilst the values generally used in CIF files do not really require such formatting, there are cases of machine-generated files using this notation, and we are pleased to further strengthen our support for the CIF format.
Miscellaneous Fixes and Enhancements. This release contains several other improvements made since the 2.6.3 release:
Removed support for the use of the plus character ('+') to designate standard uncertainty (e.s.d., or error bars) in CIF files. This was apparently used long ago by the ICSD's 'Retrieve' program, but is not officially recognized in the CIF specification; instead, standard uncertainty should be designated using parentheses, 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. Use the Window > Toolbar submenu to choose from the various standard layouts; right-click on the toolbar itself to customise the list of tools displayed.
Fixed the generation of invalid output and a possible crash when exporting visible coordination files.
CrystalMaker now displays a progress bar when loading multi-dataset files (and generating Views pane thumbnails).
Fixed a problem which could cause the wrong kind of thumbnail to be displayed in the Views pane.
When choosing a folder into which to save Views, the Folder Browser dialog now allows you to navigate above the level of the most recently visited folder.
Miscellaneous Fixes and Enhancements. This release contains a few improvements made since the 2.6.2 release:
CIF files containing data tags on the same line as the loop_ statement are now read correctly.
Fixed a crash which could occur when using the Edit > Structure command on a molecule.
When displaying atom numbers as labels, the numbering now starts at 1 rather than 0.
Sections of the End User's Licence Agreement have been reworded to improve clarity.
Miscellaneous Fixes and Enhancements. This release contains a few improvements made since the 2.6.1 release:
VASP file import now handles orthogonal ("Cartesian") coordinates correctly.
An issue that prevented the Transform > Calculate Formula & Density command from calculating densities has been resolved.
The Recent Files pane no longer accepts dropped files. Please use the new, Favourites, pane to store your custom file collections - that pane will accept drag and drop, whereas the "Recent Files" pane is automatically updated to reflect your file opening history.
Palette windows are now restored to their correct states if the app is minimised and then restored by double-clicking on a CrystalMaker file.
Elements Toolbar Menu. A new popup menu button has been added to the 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.
Miscellaneous Fixes and Enhancements. This release contains several other improvements made since the 2.6.0 release:
We now support version 5 VASP files, which allow the inclusion of atomic symbols in the POSCAR or CONTCAR file. Version 4 files, which supply this information in the POTCAR or INCAR files, are still supported.
When importing data from POSCAR/CONTCAR files which do not reside in VASP project directories (i.e., no INCAR file is present), the Graphics Window title is now set to the structure file name (typically 'POSCAR' or 'CONTCAR') rather than the enclosing directory name.
Clicking an icon thumbnail in the Favourites pane now correctly updates it to a preview thumbnail. Also, clicking on a thumbnail in the Recent Files pane will cause any corresponding thumbnail in the Favourites pane to update if necessary.
When reading rhombohedral structures from from WIEN2k files, the lattice parameters are now correctly converted from hexagonal dimensions as required.
Measurements from WIEN2k files are now converted from atomic units (bohr) to angstroms.
Attempting to add any type of file other than a CrystalMaker binary file to the Favourites pane will now cause CrystalMaker to prompt you to save the file as a CrystalMaker file.
VASP and WIEN2k file thumbnails now display the correct file type badge.
When performing cell transformations, transform matrix elements are now printed to 4 decimal places rather than 2.
The Elements toolbar button now has the correct icon.
Files of unknown type are now represented in the Overview window using a generic document icon rather than a blank space.
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:
Recent Files Submenu. CrystalMaker now includes a File > Open Recent submenu. This submenu provides a quick way of accessing recent files, and is an alternative to the Recent pane (see above) in the Overview window.
By default, the menu lists the 20 most recently opened files (the full list can be reviewed in the Overview window).
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:
Annotation text no longer vanishes when plots are exported to images with higher resolution than the screen.
The application no longer hangs when drag-selecting more than one annotation box.
Fixed a problem in which CIF files with a single data item on the same line as a data tag in a loop would not be read correctly.
Fixed a problem in which file names could be truncated or the application cold crash when saving QuickTime movies on Japanese systems.
The Graphics pane no longer goes blank following the export of a plot image.
Video recording no longer causes a crash when the user tries to save to a file that already exists and is open.
Resolved a rare case in which an incorrect origin setting could be applied when reading from a spacegroup in Full International notation.
The File > Import menu has been tidied, to make it easier to scan.
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.
Miscellaneous Changes. This version includes various other minor fixes and improvements:
Link with Existing Pattern. The new Transform > Single-Crystal Diffraction > Link with Existing Pattern command allows you to link a CrystalMaker structure to an already-opened SingleCrystal diffraction plot. This is handy if you want to do Live Rotation with a plot that was saved earlier in a SingleCrystal session file.
Installer Upgrade Warning. The Installer will now warn you if you attempt to install an upgrade of CrystalMaker over an earlier version already installed on your system.
Thermal Ellipsoid Information. Clicking on an Info button (in the tag displayed when you click on an atom using the Info tool) 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 active pane of the Overview window (which does not have to be visible, however). The Play Views Again and Play Files Again commands perform the same animation without displaying a dialog, using the existing (or default) 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 Log pane is now correctly made visible as requested when various types of log output are generated.
PDB crystals are now read correctly even if the input lines are not 80 columns wide.
The Play button in the Toolbar is now enabled or disabled depending on the state of the Overview dialog, as it should be.
Standard Toolbar configurations, which can be selected from the Window > Toolbar submenu, can now also be selected by right-clicking in the Toolbar and choosing one of the equivalent commands from the end of the active item Toolbar popup menu.
Popup menu buttons now display their menus so that the menus do not overlap the button itself, preventing the inadvertent selection of a menu item which might suddenly appear under the cursor.
Zapper tool and Snapshot command sounds are now more responsive and better able to keep up with a rapid sequence of commands. Also, the Zapper tool no longer beeps when you click an empty space.
'.txt' is no longer supported as a standard file extension for DL_POLY files, as this would override the use of the extension for text files. DL_POLY files ending in '.txt' can still be imported using the File > Import > DL_POLY command and searching for all files in the Open dialog.
Miscellaneous Fixes and Enhancements. This release contains improvements to the Transform Cell command and to the general range display:
When performing cell transformations, the lattice type of the transformed structure is now correctly identified.
Fixed a very-rare problem in which atoms too close to the unit cell edge were not shown for some range settings.
Miscellaneous Fixes and Enhancements. This release contains several improvements made since the 2.5 release:
The Transform > Transform Cell command now works correctly with primitive lattice types.
Blank thumbnails are no longer generated in the Views pane when executing the Transform > Synchronise command. Also, a synchronisation operation can now be cancelled by pressing the Escape key.
The status display at the bottom of the Overview window is again updated properly.
Drag-selecting annotation text boxes using the Arrow tool once again works correctly.
Structures are no longer rescaled following an Undo or Redo.
The default compression codec is again Animation.
Quicktime video compression settings are now retained across all Quicktime-related interfaces.
The time required to initialise the Files pane at launch with a large number of file thumbnails has been greatly reduced.
Removed support for .txt as a registered DL_POLY file extension, to avoid collision with standard text files. The Update Installer fixes the user's Registry and requires a restart.
Fixed memory leak which was most evident when creating videos from Views pane thumbnails.
Fixed a potential hang which could occur when quitting the application.
Clicking the Register Online button in the registration reminder dialog during installation again takes the user to the registration Web page. Also, the Register Online button is now the default.
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 in the Transform Cell dialog 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.
Note that the Transform > Supercell command has been removed, and its functionality subsumed into the Supercell option in the Advanced Options area of the Transform Cell dialog.
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).
AVI Video Support. Whilst QuickTime remains the first choice for professional-quality digital video, AVI format is still required for use with some Windows-based software, such as Microsoft PowerPoint. CrystalMaker for Windows now provides a choice of QuickTime or AVI output, selected using new buttons along the right-hand edge of the Video Recorder palette (Window > Palettes > Video).
Note that the choice of QuickTime or AVI made in the Video Recorder palette is retained for subsequent recordings (e.g., File > Export > Rotation Movie), and determines the type of video compression dialog that appears when requested by other commands. To change the current recording format, open the Video Recorder palette and click the appropriate button.
Full H.264 Support. When recording using QuickTime, CrystalMaker for Windows 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, JPEG 2000.
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 that of 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 STFC Daresbury Laboratory 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 visualisation, synchronisation and animation allows seamless viewing of the complete refinement trajectory: an ideal way to understand the progress of your modelling calculations!
Improved File Input and Overall Performance. In this release, file input speed has been significantly improved, and application overhead when loading all file types has been greatly reduced. The result is much faster loading of multiple files and multi-dataset files, as well as better overall performance when manipulating structures.
Also note that lengthy multi-document and multi-dataset loads can now be cancelled by pressing the Escape key.
Constrained View Direction. We have redesigned the Set View Direction window, to give the option of specifying a second direction, whose projection should be displayed vertically, from the bottom to the top of the screen. This constrains the crystal orientation.
To provide a more elegant, and less intimidating interface, the vertical constraint vector coefficient fields are initially hidden. They can be revealed using the new Constrain orientation disclosure control.
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.
(Prior to this release, 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 'jiggle', as the geometric centre shifted from frame to frame, owing to some atoms moving into or out of the plot range.)
Sortable Thumbnails. The Overview window's Actions menu includes two new commands to sort File and View pane thumbnails in ascending or descending order, according to their titles. You can still rearrange the thumbnails after the sort, and re-sort as needed by choosing the desired command.
This is useful when working with large numbers of views, especially if a set of views or files have been loaded all at once, and the operating system has not supplied them to CrystalMaker in the desired 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, and 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 various bug fixes and enhancements:
A serial number is now displayed in the About box (Help > About CrystalMaker). 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 'Windows' as your operating system!).
Wireframe plotting for Polyhedral models is now more consistent. 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.
The order of the menu items in the Selection and the Graphics pane contextual menus has been changed to provide a more consistent layout, and better reflect a typical workflow.
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 (you can also choose the Model Options command and then navigate to the Background pane, or choose the Background item from the Model pop-up menu button in the Toolbar).
In addition, you can now drag and drop picture files into the Graphics pane to set the background display.
When converting structures from 'molecule' to 'crystal' mode, an incorrect internal sorting of atoms occasionally resulted in memory issues when atoms were deleted. CrystalMaker now automatically fixes these structures as they are read and notifies the user that they should be re-saved.
Fixed a bug that caused the List Bonds command to fail when the "Search each selected site" option was checked.
Copying or exporting stereo red/blue plots no longer causes a crash.
When drawing structures as Stick models, the spheres which form the stick joints are now drawn using the correct rendering style.
Visible areas of surfaces are now correctly highlighted when selecting sites in Space Filling mode.
When switching between black & white and colour rendering modes, the label colours are now set correctly for the given background.
When creating a new structure, the default unit cell axis lengths are now 5Å rather than 10Å.
When sorting labelled sites in the Site Browser and other lists, labels which consist solely of element symbols and numeric indices now precede any labels which contain additional characters other than whitespace. E.g., the site labels 'Si(1)', 'Si(2)', 'Si 3', 'Si 4', 'Si5', 'Si6' will sort to 'Si 3', 'Si 4', 'Si5', 'Si6', 'Si(1)', 'Si(2)'.
When displaying origin offsets for GEP-based symmetry as fractions in the Edit Crystal dialog, denominators up to 1,000 will now be displayed.
If a negative isotropic temperature factor is encountered whilst reading a CIF file, a warning is generated and the value is discarded. (These nonsensical values are apparently sometimes used as marker data for other sofware.)
File > Import > MDL Molfile and MDL SDFile have been renamed Molfile and SDFile, respectively; the 'MDL' prefix has been dropped.
A problem recognising certain SDFile-format files has been corrected.
Opening the Plot Range palette with the Live Update option ticked no longer immediately causes an update of the currently plotted structure.
The contents of the Angle text box in the Calculate Angle dialog can now be selected and copied.
The Rotation Movie Options dialog (File > Export > Rotation Movie) now correctly updates the various displayed values as the number of frames and movie duration are modified.
The video frame rate is now preserved across invocations of the QuickTime compression settings dialog. Also, a problem which occasionally caused this dialog to refuse to close has been corrected.
The File > Place Molecule command is now enabled in Demo builds.
The up and down arrows for the Inner Radius and Outer Radius edit text boxes in the Define Cluster dialog now increment and decrement the values by 0.01Å rather than 0.33Å.
When saving views or performing any other action which requires browsing for a folder, the most recently visited folder is now used as the starting point in the folder browsing dialog.
If the User's Guide or Setup Guide fail to open, you can now click a button to go to Adobe's Web site to download Adobe Reader.
New cristobalite, leucite temperature factor, and amino acid structures have been added to the Crystal Structures Library, and various structures in the Zeolites group have been updated.
Miscellaneous Fixes and Enhancements. This release contains several improvements made since the 2.3.5 release.
Fixed a problem in which generating excessively long labels from large numbers of atoms read from XYZ files could corrupt memory and cause a crash.
Fixed a problem in which deleting atoms in certain structures could cause a crash.
Fixed a problem in which reading a structure into the same window as one which had more elements and then switching models (e.g., from ball-and-stick to space-filling) could cause a crash.
Warn the user if a crystal file is read whose atoms array is not properly sorted; the file should be saved after reading.
Updated Online Help for XYZ file format to reflect support for multiple datasets.
Toolbar Captions Restored. Captions can again be displayed in the Toolbar; both the Window > Toolbar > Icon and Text and Text Only commands are again available.
Some groups of tools now have a single caption; the tools can be distinguished by their icons or by passing the cursor over them to display their tooltips. In Text Only mode, each tool is individually labelled.
Note that groups of tools are removed as a unit from the Toolbar if the width of the Toolbar is insufficient to accommodate the entire group. The individual tools will appear as menu items in the overflow popup menu at the right end of the Toolbar.
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:
A problem in processing site labels which could lead to a crash has been fixed.
A problem in processing polyhedral plots which could lead to a crash has been fixed.
The labels for the Ball and Stick property fields in the Model Options dialog's Atoms pane have been corrected.
XYZ File Export. CrystalMaker now supports exporting of files in the *.xyz file format, via the File > Export submenu.
Miscellaneous Fixes and Enhancements. This release contains several improvements made since the 2.3.3 release.
Thermal ellipsoid data are now ignored on input unless at least one valid record is read.
The Status Window should appear less frequently than before.
When Uninstalling on 64-bit systems, the Shell Extension is now properly removed.
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 default (and possibly erroneous) values.
In addition to improved handling of complex syntax, the new algorithm is also able to cope with massive input files (> 100 K atoms).
Although CIF files which (incorrectly) use the same site label for different sites can now be loaded, we strongly recommend that such structures be corrected, within CrystalMaker, using the Site Browser's Generate Site Labels contextual menu command.
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.
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 Kiosk mode has been renamed 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 by right-clicking on the toolbar and choosing the Play item from the popup menu.
Miscellaneous changes. This version includes various bug fixes and improvements:
Automatic site label generation now uses either base-10 or base-16 numeric suffices, depending on the number of labels required, so as to minimise the length of the labels.
A warning dialog is now displayed before performing auto-generation of site labels and colours.
Bonds are no longer drawn in the wrong half of the image when displaying stereo views in which the left and right images overlap.
The Replace with Current View command in the View pane's Action menu works again.
Significant performance improvements have been made in various operations, and in particular when reading, writing, and displaying site information.
Fixed a crash in the Edit Structure dialog which could occur if any attempt was made to sort on a column other than the site number.
Fixed a possible memory corruption when reading Molfiles and SDfiles.
Fixed a possible hang during quit.
Fixed potentially incorrect sorts when sorting list columns in descending order.
Subtitles are again properly erased when new structures are loaded into an existing window.
When entering full-screen mode from a Main Frame window maximised on the primary display, the structure is again displayed correctly and is not clipped to the primary display.
The Window > Show Toolbar command is now disabled in full-screen mode.
When switching between thumbnails in an Overview Window pane, the selection is no longer lost if the Status Window appears.
Descriptive text in empty Overview Window panes is now drawn correctly.
Fixed a problem in which an update installation could be corrupted if the user ran the Updater more than once without rebooting when given the option to do so.
Fixed a problem which prevented updates to installations in other than the default location.
File icons are now properly installed and functional on 64-bit systems. In addition, fixed an installation problem which could prevent file icons from being displayed properly on all systems.
Support for the Status Bar has been removed.
Updated Metallic Structures files in Crystal Structures Library.
Updated User's Guide.
Improved Animation Movies. Animations, created using thumbnails from the Views pane, can now be exported as movies with or without looping (left-to-right or back-and-forth), and with full rendering quality. The looping settings specified in the Play Options dialog are also now respected when recording movies (e.g., using File > Export > Rotation Movie or using the Video Palette).
(Earlier versions of CrystalMaker allowed basic movie export, using the default rendering mode, and without looping.)
File Import Enhancements. Several changes have been made to improve the handling of various file formats:
The CIF file parser now recognises the new _database_code_amcsd tag used in AMCSD-generated files, and adds the associated text to the Notes pane.
When importing PDB files, we now merely skip the input line if the element ID is invalid, and display a warning in the Log rather than aborting input.
Subtitles indicating that warnings generated during file import have been written to the Log pane are again displayed following the initial plot of the loaded structure.
Miscellaneous Fixes and Enhancements. A number of problems have been corrected, and other improvements made:
Fixed a bug which could cause the program to hang when loading Views and switching quickly between the Views and Files panes of the Overview window.
Fixed a crash which could occur if an Overview pane was not visible and more than one row's worth of views were added (e.g., by clicking the Snapshot button multiple times whilst the Views pane was hidden).
Fixed a crash which could occur if the Overview window were displaying no thumbnail images.
Fixed a problem in which an unused file icon appeared in the Graphics window title bar when loading cached View or History files, or in the Views pane when loading large numbers of files.
If a file fails to load correctly into a Graphics window which is already displaying a structure, the original data are restored.
Improved performance when loading multi-dataset files.
Flicker in the Tool palette structure button has been greatly reduced.
Overview panes are updated correctly even when the program is shutting down (e.g., if a 'save file' dialog appears as the program is quitting).
New structures added to the Crystal Structures Library. The minerals Painite and Nosean have been added to the Library.
Installer improvements. Fixed an application initialisation problem which could cause the Installer to fail to properly register file associations or to fail to install at all.
Improved Overview Window. Various issues associated with large numbers of files or "views" have been addressed. These include:
Miscellaneous Fixes and Enhancements. Various performance and memory improvements have been made in this release, which also address the following issues:
Fonts (and plot axes and gridlines) are now scaled correctly when copying or exporting graphics.
Fixed a problem which could cause occasional crashes when quitting the application.
Fixed a problem which caused the app to hang during rotation or user manipulation of the structure.
Fixed a problem which could cause a crash when dragging and dropping multiple files at once onto the application icon.
Improved handling of low-memory conditions, allowing execution to continue if a large memory request fails but there is sufficient memory available for other tasks. Also fixed a problem which could result in an invalid memory reference and probably a crash under low-memory conditions.
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'.
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 duplicated the existing Window > Palettes > Video command.
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.
Improved Data Input Performance. Significant changes have been made to the file I/O subsystem which should improve performance when reading files with multiple datasets, animating Views and Files pane thumbnails, and performing Undo and Redo operations.
Miscellaneous Changes. This version includes numerous subtle enhancements and some bug fixes:
The default frame rate for QuickTime movies has been increased from 6 to 12 frames per second (fps).
QuickTime frame rates and Rotation Movie settings are now automatically saved in the user's Preferences.
Database codes are now extracted from AMCSD-derived CIF files, and copied to the Notes pane (and the window title, if appropriate).
Labels are again correctly scaled when copying or exporting images (File > Export > Graphics or Edit > Copy Graphics).
SHELX files that omit site-occupancy fractions and isotropic temperature factors, can now be read.
Fixed a crash which occurred when calculating polyhedral geometries during deletion of atoms when the minimum bond distance had been set to a value other than 0.
When reading CIF files, hash ('#') and underscore ('_') characters are now handled correctly.
The Status Window now updates progress messages more reliably.
Detection of SHELX file types is now more robust.
A new edition of the CrystalMaker 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.
Several structure files have been added to the Crystal Structures Library.
Improvements to File Handling. This version includes changes to the way in which CIF files are imported and exported and better auto-detection of SHELX files.
Improved Graphics Rendering and Export. The graphics export has been improved, and various scaling problems are now resolved.
User-Interface Enhancements. Various subtle changes have been made to the interface to improve the look-and-feel and improve system compatibility.
Miscellaneous Changes. This version includes numerous miscellaneous enhancements and bug fixes:
New File Export Options. New text files can now be exported from CrystalMaker, giving you more options when you need detailed information about your structures.
The File > Export > Visible Coordination command generates a text file that summarizes the connectivity of the displayed structure.
The Visible Coordination text 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.
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 text 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 atom site visibilities.
Notes Pane Improvements. Several improvements have been made to the behaviour of the Notes pane in the Graphics window:
Miscellaneous Changes. This version also includes various other miscellaneous improvements and bug fixes:
Installation and Licensing Improvements. Substantial changes and upgrades have been made to the Installer and Updater software, to improve general performance and stability, and for improved compatibility with Windows Vista, roaming profile accounts, and installation by non-Administrator users.
Resetting from single- to multi-user license codes using the Help > Reset Licence command is now handled correctly. The user will be asked to quit the application; the licence change will be performed, and any necessary files moved to new locations as appropriate (e.g., the Examples folder will be moved either to the user's or the All Users documents folder).
Other changes to the way installations and updates are handled include the following:
Users are now alerted 14 days (rather than 10) before a licence is due to expire.
The user's My Documents folder, which may be located on a remote share, is now correctly identified.
File associations are now always stored on a per-machine basis. Individual user associations are still maintained by Windows.
Following installation of multiple applications from the CD-ROM, CrystalMaker now remains the default application for handling its file types. Any changes made by the user after installation are respected, unless the application is re-installed.
Automatic uninstallation of earlier versions is now more reliable, and no longer require system restarts as often.
The Installer log file (often useful when contacting Technical Support), is now stored in the CrystalMaker Software folder in the Common application data folder, and is updated by any user's installation. Existing logs are merged into the common log on update.
User name and organisation strings passed on the command line to an Installer (usually for silent installations), are now properly stripped of leading and trailing quotation marks.
A number of spurious run-time errors have been eliminated.
NOTE: Non-administrator and roaming profile users may wish to re-locate their existing Examples, Crystal Structures Library, and Multimedia folders, which may have been installed in incorrect locations.
NOTE: Users who have purchased (not updated to) version 2.2.0 and have installed it for All Users should contact Technical Support.
Miscellaneous Fixes and Enhancements. This release contains a number of significant fixes and improvements. Among these are the following:
Rotation with Arrow Keys. Rotation can now be performed using the arrow keys when the Rotate tool is active. Rotation applies to structure or selection, depending on state of Rotate All/Rotate Selection setting, and can also be used in temporary rotation mode (when the space bar is held down to temporarily activate the Rotate tool). Left and right arrows rotate about the screen Y axis; up and down rotate about the screen X axis. Holding down the shift key whilst pressing any of the arrow keys, rotates about the screen Z axis.
Installer Improvements. The following changes have been made to the Installer and Updater to correct their behaviour on certain installations, particularly those involving Roaming Profile accounts or multi-user licences:
Stability Improvement. A potential problem, due to a bug in Microsoft libraries used by CrystalMaker's shell extension, in which the Windows Explorer could occasionally hang when displaying CrystalMaker binary file icons, has been corrected.
Spectacular Red/Blue Stereo. CrystalMaker now supports red/blue colour stereo plots, as well as enhanced, high-contrast stereo plots in greyscale and black-and-white rendering modes. To view coloured 3-D stereo models, 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 filtered out by the right and left lenses, respectively, of your red/blue spectacles). For best results, choose colours with hues that are intermediate between red and cyan (i.e., the colour ranges orange-green and indigo-blue).
Comprehensive New Background Gradients. The Background pane of the Model Options window now provides extensive new gradient shading options. The old Up and Down gradient options have been replaced by a Linear gradient, and the Inward and Outward options have been replaced by a Diamond gradient. Two brand new options, Radial and Reflected, plus new Angle and Scaling sliders, give professional-level control to your model display.
Gradient starting and ending colours can be now be specified independently of the 'plain' background colour, and clicking the double-arrow 'flip' button quickly swaps the start and end colours.
Gradient fills specified in existing CrystalMaker binary data files will be converted to the new format so as to preserve the previous appearance as much as possible.
Live Model and Rendering Controls. You can now adjust almost all Model and Rendering Options settings in real time by holding down the Control key as you click a button or adjust a slider control in any of the panes in the Model Options or Rendering Options windows.
Model, Rendering, and Overview Toolbar Menus. The Model, Rendering, and Overview toolbar buttons are now clickable popup menu buttons: Click the button as usual to toggle the display of the palette window; click and hold to display a popup menu to display specific panes.
Disposable Thumbnails. Any thumbnail image in the Files, Views, or History panes of the Overview window can now be deleted simply by dragging it out of the pane and releasing the mouse button (this is in addition to the standard Delete menu option in the Overview window's Action popup menu button).
Updated Crystal Structures Library. New organic molecules have been added to the Crystal Structures Library: taurine, pyridoxine, pantothenic acid (vitamin B5), niacin (vitamin B2), and aspartame.
Installation Enhancements. A number of significant enhancements have been made to the CrystalMaker Installer and Updater:
Miscellaneous Changes. This version includes a number of minor changes and bug fixes, including the following:
Extended Density Calculations. The Transform > Calculate Formula & Density command 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.
The File > Export > Bond Data now generates density information as well.
File Handling Changes. Shortcuts (links) to data files or folders can now be dragged and dropped onto the Graphics or the application icon; links contained within dropped folders will also be resolved.
All Open and Save File dialogs now track the file type most recently selected by the user, and the last directory to which a file was saved.
Improved Main Frame Window Dynamics. The Main Frame window can now be resized across multiple displays, either by dragging its edges, or by clicking its maximize button - or in Full-Screen mode.
Please note that when the Maximize command is used, the Main Frame will expand to fill the nearest display.
When entering Full-Screen mode, the Main Frame window will occupy the full virtual desktop, covering all displays. You should ensure (using the Display control panel under XP or the Display Settings control panel under Vista) that the primary display is aligned at the top of the virtual desktop so that the items in the drop-down menu bar will be accessible when the mouse is moved to the top of the display.
Enhanced Colour Picker. The colour picker window, displayed when a colour selection button is clicked, now shows a suite of standard CrystalMaker-specific colours. The new picker also displays custom colours and retains them across application launches.
You can define custom colours by clicking the More Colours button in the picker, and using the standard Windows Colour dialog to add colours to the custom colour set.
A minor issue in which the colour picker and dialog were not displayed on secondary displays has been corrected.
Workaround for Ad-Aware Issue. A bug in a recent version of Lavasoft's Ad-Aware anti-malware utility caused a kernel memory leak, which was especially noticeable whilst using CrystalMaker products for Windows. This release mitigates the problem significantly; it should no longer be a major issue for users who have Ad-Aware installed on their systems.
Lavasoft are aware of the problem, and will shortly be releasing an update to their software that fixes the problem. Users of Ad-Aware are strongly urged to download and install the update as soon as it becomes available.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Help Viewer. A new Help Viewer window is now available for the online help system. This floating window allows help topics to be displayed within the program, without disrupting the window visibilities, and without requiring use of an external program (such as a web browser).
Choosing any online Help item from the Help menu opens the new Help Viewer. As with other floating (palette) windows, this window remembers its position and visibility, and loads the last Help page visited when opened.
Clicking on a link to an Internet-based Web page (or any other file which lies outside the CrystalMaker Help folder, or which is not HTML) will open a default application.
Improved CIF and SHELX Support. CrystalMaker can now process special-case SHELX files with constrained or refined site occupancy data. 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).
In addition, when reading CIF and SHELX files, site occupancies are now sorted in descending order by occupancy ratio, ensuring that sites are associated with the dominant element.
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., the structure is not a molecular crystal), the previously displayed structure is now correctly restored.
Improved Support for Multiple Displays. All window positions, including those of palette windows, are now correctly calculated, retained, and restored on systems with multiple displays.
When entering full-screen mode, the application will now fill the screen of the display on which most of the Main Frame window resides.
Model Options Enhancements. Several changes have been made to the performance and appearance of the Model Options dialog:
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Assemble Views using Drag-and-Drop. Window views can now be created simply by dropping any CrystalMaker binary 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 drop the files you need directly into the Views pane. Each file is loaded into the current 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 Open File dialog to select your files.
Window views can be synchronised, rearranged, updated, or deleted before being displayed as an animation (Actions > Play) or exported to a movie (Actions > Save as Movie).
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:
Edit Bonding Changes. The Auto Set Range checkbox has been removed from the Edit Bonding dialog, to simplify the interface. When a bond is created, CrystalMaker will use the sum of the element radii to calculate an appropriate maximum bond length (which can then be edited).
In addition, a problem in which coordination information was not properly initialised for certain classes of bonds has been corrected.
Improved Shell Interaction. CrystalMaker now uses an improved mechanism for handling dropping of files onto the application's icon or double-clicking of files from Explorer windows. This should result in better performance and reliability, especially on Windows Vista.
Performance Improvements. Significant improvements to performance have been made in a number of areas, including:
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
Torsion Angle Signing. Torsion angles, measured using the Torsion Angle tool, 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 anticlockwise rotation.
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:
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.
An additional feature is that ATOMS files with *.str extensions can now be loaded using the File > Import command (although most users will probably prefer to use the File > Open command, or drag-and-drop).
Extended CIF Output. Site occupancy data and atomic displacement parameters ('thermal ellipsoids') are now exported to the CIF format.
Miscellaneous Changes. This version includes a number of minor changes and bug fixes:
User Interface Enhancements. All Views created when opening a multi-dataset file are now numbered, making identification easier. In addition, a problem whereby thumbnails would vanish following cancellation of a 'Save Changes' alert (during quitting) has been resolved.
Other interface changes include an improved window toolbar, with new separator lines and improved popup menus (arrows no longer overlap text in 'Text Only' mode).
Live Rotation Link with SingleCrystal. This version of CrystalMaker and a new version of SingleCrystal (1.1) can be linked so that rotating a crystal structure in CrystalMaker causes the corresponding diffration pattern in SingleCrystal to rotate (and vice versa). The 'live rotation' can be toggled on or off, via the Transform > Diffraction Pattern > Live Rotation menu.
New Plane-Fitting Algorithm. The Transform > Lattice Plane > Fit Through Points command uses a more accurate starting model, with a subsequent least-squares refinement process, resulting in more precise and reproducible results.
New Porosity Calculation. The new Transform > Calculate Porosity command calculates the amount of free space in a crystal. The result depends on your currently-specified atomic radii, so you may wish to edit your settings before you choose this command (e.g., via the Edit > Elements command).
CrystalMaker uses geometric considerations to calculate the precise amount of free space, taking into account the atomic volumes and any nearest-neighbour intersections (this is not an 'available space' algorithm). Please note that this algorithm is not designed for extreme cases with over-large atoms causing multi-neighbour intersections.
New File Formats. CrystalMaker now supports importing of version 4 and version 5 ATOMS files, as well as Molfile and SDfile formats from Molecular Designs Limited (MDL, now owned by Symyx).
Window Toolbar. The Graphics window now supports a toolbar which provides 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.
The toolbar can be extensively customised, using a contextual menu. Alternatively, three pre-set layouts are available from the Window > Toolbar submenu.
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.).
Open Multiple Files as Separate Views. Opening multiple CrystalMaker binary files into the same Graphics window now results in each structure being opened, as a separate view, in the same window.
Save Window Views. A new Save Views item in the Overview window's Actions menu results in each window view being saved as a CrystalMaker binary file.
Revised Element Editor with Live Switching. A new Live Update checkbox has been added to the Element Editor window (Edit > Elements). With this option enabled, you can browse different element tables (e.g., via the window's popup menu), with your structure automatically replotted.
A new 'SAR Covalent Radii' element table file has been added to the standard installation, and is available for selection in the Edit Elements window. This table, (provided courtesy of Prof. Santiago Alvarez, University of Barcelona), gives updated covalent radii values.
Lattice Plane Support in 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.
New Animation Option. When choosing the Play command from the Action menu in the Overview window, you can now choose between either unidirectional (left-to-right) or bidirectional (back-and-forth) looping.
Synchronise Again Toolbar Option. Users can now synchronise more quickly, suppressing the Synchronise Options sheet, and using the last-specified settings. Simply hold down the shift key whilst pressing the Synchronise toolbar button.
New Plot Range Controls. New controls allow easier adjustment of plot ranges in the Plot Range window ( Transform > Set Range). Multiples of unit cells can easily be added or removed, and there is the option of automatically rescaling the resulting structure to fit within the Graphics pane.
More Powerful Spacegroup Recognition.
Spacegroup symbols that use parentheses
to designate subscripts (International
notation) can now be recognised. For example,
P 2(1)2(1)2 for
P 21 21 2.
This should mean that CIF and other file formats
(e.g., originating from Bruker) are
easier to load.
Performance and Usability Enhancements. A number of existing features have been improved or had new capabilities added:
Improvements and Fixes. A number of outstanding issues have been addressed in this release:
New Help Menu Features. The Help menu now includes two new commands, giving access to a PDF version of the printed Setup Guide, and easy access to the 'What's New' section of the Online Help. Another improvement is that pressing the F1 key should no longer open multiple Help windows.
Faster File Import. Multi-structure PDB and CIF files are now loaded up to four times faster than before. In addition, the Overview window's Files pane now receives dropped files ten times faster than before, making it easier to build up file collections and browse them.
Smooth Site Browser Updates. The Site Browser (both in the palette window and the Sidebar pane in the Graphics window) now behaves less obtrusively: flicker in the Site Browser when loading structures has been greatly reduced, improving appearance and performance.
More Flexible Installation. The CrystalMaker for Windows Installer now allows installation by users who are members of the Power User group, in addition to Administrators.
Flicker-Free Video Recording. The Video palette controls are now updated more reliably and no longer flicker during recording. Switching between two identically-sized Graphics windows during a video recording no longer causes the image from the window not being recorded to appear in the movie. Closing a Graphics window in the middle of a video recording no longer causes a crash.
Better Spacegroup Handling. In the Spacegroup Browser, clicking on a spacegroup item after clicking the Show All Settings checkbox no longer causes the list to scroll to the top and lose the selection. Spacegroup symbols are no longer converted to full international format when being written out to CrystalMaker binary files; the user's specification is preserved.
Vista List-Editing Bug. On Windows Vista, editing scrollable lists could be problematic, as the system caused the list to scroll back to the first column when an editable item was clicked - with the possibility that the editable item was scrolled out of view. This problem has now been addressed, and horizontal/vertical scrollbars now appear as required. In addition, pressing the Escape key now ends an editing session and discards any changes.
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. Various additional, miscellaneous improvements and bug fixes have been included in this release:
Improved Drag-and-Drop Behaviour. When dropping a file into a Graphics pane, the associated Graphics window is now brought to the foreground and the file opens in the target window as expected.
Dropping files or folders into the Graphics pane now loads the files into the same window sequentially and adds their thumbnails to the Files pane. (Dropping files into the Main Frame background opens the files in separate windows.)
Revised Sidebar Control. When switching Workspaces (using the Window > Workspace menu commands), the Notes and Site Browser (Info) panes are now shown or hidden as appropriate to the Workspace.
The Sidebar pane states are preserved when switching out of Full Screen mode, or when opening new Graphics windows, and the Window > Sidebar menu now behaves correctly.
Improvements to Auto Rotation. The Auto-Rotation dialog now checks to ensure that the oscillation period is greater than the rotation interval. The menubar is now hidden during auto rotation in Full Screen mode; pressing the Escape key will now cancel the auto rotation (press Escape again to leave Full Screen mode).
More Seamless Synchronization. Improvements have been made to the design of the Synchronise dialog, and to the subsequent behaviour, so as to make the entire operation more seamless and responsive.
When synchronising window Views, the Graphics window is updated more cleanly, with View thumbnails refreshed in sequence, thereby providing feedback as to the progress of the operation. An issue relating to synchronization for a maximised Graphics window, has also been resolved.
Enhanced Play Command. The Play command, available from the Actions menu in the Overview window, has been refined, and no longer results in generation of spurious History events, or a progressive slowdown in performance over time. Cancelling Kiosk mode no longer results in palette windows being hidden, or dimming of items on the Window > Palettes submenu.
Miscellaneous Changes. Various additional, miscellaneous improvements and bug fixes have been included in this release:
Improvements to Spacegroup Handling. The Spacegroup Browser has been improved in two ways: unconventional spacegroups are displayed using Short International symbols (where possible), and a problem which could cause the application to hang when searching for particular spacegroups has been fixed.
General equivalent positions, specified using floating-point offsets (as opposed to the more usual fractional form) can now be read from SHELX and other text files.
User Interface Enhancements.
Improved Tool Tip Support. Tool tips have been re-enabled for the Tools palette, and tooltips are now available for virtually all dialog and palette windows.
Installer Enhancements. A number of improvements have been made to the Installer and Updater to ensure a more consistent and stable application environment.
Miscellaneous Changes. A potential memory corruption problem, arising from the import of one or more invalid text data files, has now been fixed.
This version has no new functionality but does fix a problem with an expiration date that had inadvertently crept into the shipped program.
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.
Installer and Updater Enhancements. The Installer is now more flexible, allowing installation of non-core components without overwriting an updated application.
Improved Printing. Printing from CrystalMaker has been improved to ensure that output is correctly scaled to fit the page. Both red-blue and stereo-pair plots are now printed correctly. Rendered bond cylinders and textboxes with lines are both now output correctly.
Video Output. A number of improvements have been made to video output. Video output quality can now be previewed, using the Compression Options dialog. Linear and QTVR movie frames are again recorded properly, and the Video Recorder palette's controls are now updated correctly following the completion of recording.
Annotation Issues Addressed. The Selection > Select > Textboxes command now correctly selects all annotation objects; the Edit Annotation palette is now correctly displayed, and annotation objects are correctly scaled in stereo-pair plots.
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 release includes a number of minor changes and bug fixes, which are listed below:
Save Files command. A new Save Files command has been added to the Action menu in the Overview window. This sequentially opens and re-saves all files represented in the Files pane, allowing you easily to update your CrystalMaker binary files to the latest format (with the added benefit of embedded file previews).
More Play Options. 0.1, 20, 30 and 60-second intervals have been added to the Time per structure menu in the Play Options dialog.
Easier File Favourites. The Overview window's Add (+) button is now enabled for the Files pane. This allows you to add files to the Files pane using a standard file dialog.
Miscellaneous changes. This release includes a number of minor changes and bug fixes, which are listed below:
Workaround for editing issues. Tabbing while editing to the last column of the Edit Molecule dialog no longer crashes the application. Tabbing between list control fields in Windows Vista now works. Editing of cell parameters in the Edit Crystal dialog now works correctly and the Backspace and Delete keys can now be used in this dialog.
Vista document icon fix. CrystalMaker document icons now correspond to the correct document types, and double-clicking CrystalMaker data files will now launch the app and open the file as expected.
(Note that drag-and-drop of multiple files onto an unlaunched application icon under Vista is not entirely reliable, and will be addressed in a future release.)
Miscellaneous changes. A number of minor issues have also been addressed in this release:
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.
Depth Profiling. This new feature allows you to easily visualize the interior of a bulk material. You can profile the material's structure, by controlling the vertical extent of material to be shown at any time. Atoms "in front" of the slab can be hidden completely, or made translucent; atoms beneath the slab can be faded into the background.
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.
.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
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
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, 
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)
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 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).
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!
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).
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.
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.
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 "Lab" licences now use active licence checking technology. Users upgrading their licences (e.g., from a lab licence to a personal licence, or increasing the user limit of a lab licence) can now use the new CrystalMaker > Reset Licence command.