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CrystalMaker

CrystalMaker® 8 for Mac: Version History

CrystalMaker 8.1.4

Released: 15 September 2008

  1. 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:

    • Description: atom number, site label, occupancy)
    • Coordination details: number and number of bonds plotted
    • Polyhedral data (if relevant): number of faces and vertices, plus volume
    • Table of coordinates and distances to bonded neighbours
    • Table of bond angles and distances

  2. 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.

  3. 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).

  4. 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.

  5. Miscellaneous Changes. This version includes a number of minor changes and bug fixes:

    • Fixed an "error of type -50" problem when printing to certain printers with higher resolutions.
    • The Print Preview dialog has been improved, and now provides real-time update for print size fields or the print title.
    • Fixed a program freeze when using the Transform > List Bonds command for a structure with more than 32,000 sites.
    • Specifying a bond search, via the Transform > List Bonds command, now results in the Log pane of the Overview window being made visible, so that the output data can be immediately viewed.
    • When using the Edit Crystal sheet on Mac OS X "Leopard", the use displacement parameters checkbox is now correctly set.

CrystalMaker 8.1.3

Released: 11 August 2008

  1. Extended CIF Output. Site occupancy data and atomic displacement parameters ("thermal ellipsoids") are now exported to the CIF format.

  2. 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.

  3. 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.

  4. Miscellaneous Changes. This version includes a number of minor changes and bug fixes:

    • ATOMS file import has been improved, to cope with longer, user-supplied site labels.
    • Licensing data are displayed in the Log pane of the Overview window on startup.
    • Citation information has been added to the User's Guide and online help.

CrystalMaker 8.1.2

Released: 7 July 2008

  1. 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.

  2. 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.

  3. 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.

  4. Miscellaneous Changes. This version includes a number of minor changes and bug fixes:

    • A potential memory issue, arising from corrupted data in old-format CrystalMaker binary files, has now been resolved. If corrupted data are detected, a warning message will be displayed in the Log pane of the Overview window.
    • Optimize Range commands can now cope with structures that contain non-bonded atoms located on unit cell faces.
    • The default toolbar choice is now always visible immediately after creating or opening a new window.

CrystalMaker 8.1.1

Released: 4 June 2008

  1. Loop Back and Forth. The Overview Play command now gives a choice of looping, either unidirectional ("left-to-right") or bidirectional ("back-and-forth").

  2. 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:

    • Drag-and-drop a group of files, or a folder containing multiple files, into the same Graphics pane;

    or:

    • Choose the File > Open in Same Window command, and specify more than one file. (To choose this command, hold down the shift key when displaying the contents of the File menu.)

    Please note that opening a single-structure file does not automatically add a view to the Views pane.

  3. 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.

  4. Miscellaneous Changes. This version includes a number of minor changes and bug fixes:

    • The Quick Tour PDF document has been extensively revised, including new illustrations and discussion of version 8.1 features.
    • Chem3D ".cc1" and ".cc2" file extensions are now recognized.
    • The Set Scale sheet now has its text field focused, when first displayed.
    • The Overview Play Options dialog now includes more presets for the "Time per structure" field.
    • A problem in which automatic file format recognition supported only official file extensions, has been fixed. Any text file can now be scanned for its file format, regardless of its file extension. Please note, however, that for the quickest file import, we recommend that the official file extensions are used. recognition,

CrystalMaker 8.1.0

Released: 9 May 2008

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.)

  6. 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.

  7. 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.

  8. 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.).

  9. 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.

  10. 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:

    1. Choose the Transform > Calculate Angle command to display the Calculate Angle window.
    2. Select the atoms in one ring, using the Arrow, Lasso or Polygon tools
    3. Choose the Transform > Lattice Plane > Fit Through Points command. The best-fit orientation is shown.
    4. Locate the popup menu, to the right of the Direction 1 fields, and choose: Use Displayed Lattice Plane. The indices of the current plane are displayed in the Direction 1 fields, and this direction is set as a lattice plane normal.
    5. Repeat steps b-c for the second ring.
    6. Locate the popup menu, to the right of the Direction 2 fields, and choose: Use Displayed Lattice Plane. The indices of the current plane are displayed in the Direction 2 fields, and the angle between the two planes is printed at the bottom of the window.

  11. 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.

CrystalMaker 8.0.4

Released: 1 April 2008

  1. 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.)

  2. 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.

  3. 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).

  4. 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.

  5. Miscellaneous Changes. This version includes a number of minor changes and bug fixes:

    • A potential memory issue, related to the repeated use of the Zapper animation sound, has now been resolved.
    • Clicking and releasing the mouse with the Lasso tool active no longer results in a portion of the structure being selected. (To select a region, users should click and drag with this tool.)

CrystalMaker 8.0.3

Released: 12 February 2008

  1. 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.

  2. 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).

  3. 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.

  4. Miscellaneous Changes. This version includes a number of minor changes and bug fixes:

    • The Help menu has been rearranged, to make the more commonly-used items easier to find.
    • The licence agreement text has been reworded to emphasize the restrictions of certain licence types.
    • A rare issue involving invalid atom records saved in a CrystalMaker binary file has been addressed.

CrystalMaker 8.0.2

Released: 24 January 2008

  1. 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.

  2. 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.

  3. 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.

  4. Miscellaneous Changes. This version includes a number of minor changes and bug fixes:

    • The Help menu has been rearranged, to make the more commonly-used items easier to find.
    • A warning dialog is now shown if a user attempts to launch the CrystalMaker Update version without having first installed the full program.
    • The Change Atom Type and Duplicate Selection menu commands are now disabled when working with a crystal structure.
    • The Selection > Atoms > Style submenu now functions correctly.

CrystalMaker 8.0.1

Released: 11 January 2008

  1. 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".

  2. Miscellaneous Changes. Minor updates have been made to the online help and Quick Start guide.

CrystalMaker 8.0.0

Released: 7 January 2008

  1. New version This program is a major new version of CrystalMaker, providing the ability to work rapidly browse through massive numbers of structures, make animations, slideshows and movies. Other key features include editable thermal ellipsoids, thermal ellipsoid/sphere override, PDB crystal input and much more...

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