CrystalMaker 2.1.0

Released: 25 August 2008

Numerous new features, enhancements, and improvements are available in this major new update:

1. 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.

2. 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.

3. 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.

4. 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).

5. 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 customized, using a contextual menu. Alternatively, three pre-set layouts are available from the Window > Toolbar submenu.

6. 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.).

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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 shift key whilst pressing the Synchronize toolbar button.

13. 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.

14. 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 (e.g., originating from Bruker) are easier to load.

15. Setup Guide. A handy setup guide is now available via Help > Setup Guide . Also, you can read about the latest new features by choosing Help > What's New .

16. Performance and Usability Enhancements. A number of existing features have been improved or had new capabilities added:

    • The Transform > Calculate Angle window now displays data with up to 5 decimal places, allowing more precise data entry.
    • Icons in Tools palette buttons and elsewhere in CrystalMaker are now drawn much more smoothly.
    • File I/O performance has been improved significantly; in most cases, reading both CrystalMaker binary files and text files is from 5 to 8 times faster than before. This greatly improves opening of multi-structure files.
    • Substantial improvements to the mechanism by which Graphics windows are opened and initialized greatly improves performance and stability.
    • The CPK Element Tables now specify a darker colour for carbon atoms.
    • CrystalMaker now properly handles file types with multiple extensions. Among others, the Chem3D *.cc1 and *.cc2 file extensions are recognised.
    • Basic licence information is now printed to the Log pane in the Overview window on application launch.
    • Synchronising atom colour, radius, and style information between Graphics windows now synchronises for all matching element symbols, taking into account whether the site labels match.
    • Transform > Lattice > Hide now has Shift+Ctrl+Alt+/ as a shortcut for convenience.
    • The Video palette no longer flickers when no recording is being performed and the frontmost Graphics window is performing auto-rotation. Also, Video palette controls are updated much more reliably.

17. Improvements and Fixes. A number of outstanding issues have been addressed in this release:

    • A crash which occurred when editing a structure with a single site (deleting and then adding back the site) in the Edit Crystal or Edit Molecule dialogs has been fixed.
    • Fixed a crash which occurred when deleting bonds in the Edit Bonding dialog when the number of bonds was more than would fit in the list.
    • Fixed crashes which could occur as a result of closing a Graphics window in the middle of a video recording.
    • Fixed a hang which could occur on launch if the Graphics window's default size was too small to allow the Site Browser to be made visible.
    • The application no longer crashes if bonds are edited following a synchronisation of bond data across Graphics windows.
    • Duplicate elements in a site occupancy are no longer generated when importing CIF data.
    • Files containing unsorted molecular data are now read correctly (i.e., by element and site label).
    • Edit Elements window's Element Set popup menu now properly sets itself to "Custom" whenever the contents of the element set are edited.
    • The Graphics window Ruler again properly initialises its text and divider colours.
    • Fixed a timing-sensitive problem which could cause the Edit Crystal or Edit Molecule dialog to open when opening very large structures.
    • Pressing the Delete or Backspace key to delete a selection in the Graphics pane now works reliably.
    • The Site Browser pane and other pane states are again preserved and restored as expected when opening new Graphics windows.
    • Spacegroup symbols are no longer converted to full international format when being written out to CrystalMaker binary files.
    • Switching between identically-sized Graphics windows during a video recording no longer causes the non-target window's graphics to appear in the movie.
    • Synchronising views with a maximised Graphics window now works correctly.
    • Choosing Save Files List from the Action menu in the Overview window now actually saves the files as expected.
    • When plotting striped or hatched atoms, the centre line is no longer drawn heavier than the other lines.
    • The app no longer complains at launch if preferences it expects to see are not present; it now silently uses the default values.
    • Opening of multiple online Help browser windows when F1 is pressed is even less likely now.
    • Fixed a problem with alert dialogs which could cause the user to be unable to click the dialog controls.
    • A number of accelerator (keyboard shortcuts) have been corrected.

CrystalMaker 2.0.8

Released: 23 June 2008

1. 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.

2. 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.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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.

8. 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.

9. Miscellaneous Changes. Various additional, miscellaneous improvements and bug fixes have been included in this release:

   • Pressing the Enter or Return key whilst editing thumbnail captions in the Views pane now ends the editing session and preserves the changes; pressing the Escape key cancels the edit and discards the changes.
   • When navigating through Overview panes with the arrow keys, the Graphics window is now updated as each thumbnail is traversed, providing full animation. If a structure with selected items is loaded during navigation through thumbnails whilst an arrow key is held down (as a repeating key), the selected items no longer move; navigation through the thumbnails continues as expected.
   • The Overview panes no longer clear the currently selected thumbnail when the user clicks in the Actions popup menu button or in another palette window.
   • Choosing the Save Files List command in the Overview window's Actions menu now saves the files as expected.
   • Choosing Transform > Define Supercell and clicking Cancel in the dialog now leaves the structure unchanged, as expected.
   • Polyhedral plots with sites that have the "Sphere + Stick Bonds" style are now displayed correctly, even when some sites are only partially bonded.
   • Drag-and-drop target highlighting has been improved.
   • The progress bar is now updated correctly when saving structures with large numbers of polyhedra.
   • When using Selection > Atoms > Labels to Textboxes, the colour of the text in the new textbox now matches that of the label.
   • Deleting bonds in the Edit Bonding dialog when there are more bonds than will fit in the dialog window no longer crashes the application.
   • Removing the sole site of a single-site structure, adding a new one, and clicking OK in the Edit Crystal or Edit Molecule dialogs no longer crashes the application.
   • Launching CrystalMaker when the Graphics window default size is too small to allow the Sidebar to be made visible no longer causes the application to hang.
   • Fixed a problem with CrystalMaker's alert dialogs which could cause the user to be unable to click the dialog controls if the alert is displayed during a mouse-dragging activity (such as resizing the window).

CrystalMaker 2.0.7

Released: 23 April 2008

1. 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.)

2. 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.

3. 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).

4. More Seamless Synchronization. Improvements have been made to the design of the Synchronize 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 maximized Graphics window, has also been resolved.

5. 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.

6. Miscellaneous Changes. Various additional, miscellaneous improvements and bug fixes have been included in this release:

   • A problem which could affect the conversion of lattice planes to vectors for structures read from CrystalMaker binary files has been corrected.
   • Ellipsoid checkboxes in the Atoms list of the Model Options dialog are now set correctly. (Sites with checked ellipsoids will be displayed as thermal ellipsoids; unchecked sites will be displayed as small spheres.)
   • The New Window with this View command now works correctly for a newly-opened structure (i.e., when no history event has been generated). Structures are correctly scaled when using this command.
   • Tools that make use of "rubber-banded" lines (e.g., the Distance tool) now display the lines properly in Full Screen mode.
   • Palette windows located at or near the top of the primary display when CrystalMaker quits are no longer shifted down when the application is relaunched.
   • The state and position of the Taskbar are now taken into account when ensuring that windows are visible on the Desktop when launching CrystalMaker.
   • The Plot Range palette controls are correctly enabled when opening certain structures.
   • Thermal ellipsoid octants now have more subtly-defined traces.
   • Using the Add ("+") button to add files to the Files pane now ensures that invalid files are not added to the pane.

CrystalMaker 2.0.6

Released: 31 March 2008

1. 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.

2. User Interface Enhancements.

   • Pressing F1 whilst a modal dialog with no associated help is in the foreground now brings up the default Help page in the user's Web browser. Also, pressing F1 no longer results in two of the same help page being opened in the Web browser.
   • The correct tool cursor is now restored when the mouse is over the Graphics Window and the wait cursor is removed.
   • Changing the colour of an atom or site in the Site Browser now immediately updates the colour of the icon in the browser.
   • The About Box is now drawn with a white background.

3. Miscellaneous Changes.

   • The Installer will now detect an existing All Users installation and give the user the option to uninstall it.
   • Fixed possible memory leaks involving rendering of surfaces.
   • Bonds no longer cross the divide between halves of stereo mode images.
   • Plain bonds are now rendered with depth fading taken into account.

CrystalMaker 2.0.5

Released: 10 March 2008

1. Improved Tool Tip Support. Tool tips have been re-enabled for the Tools palette, with new tips added to virtually all dialogs and palettes.

2. Installer Enhancements. A number of improvements have been made to the Installer and Updater to ensure a more consistent and stable application environment.

   • When performing a major version upgrade, the Installer now requires that the previous version be uninstalled first, and will do this automatically for you.
   • The Updater will now automatically select the correct installation context (single-user or All Users); if you wish to change the type of installation, you will have to uninstall and then re-install from your CD-ROM.

3. Miscellaneous Changes. A potential memory corruption problem, arising from the import of one or more corrupted text data files, has now been fixed.

CrystalMaker 2.0.4

Released: 12 February 2008

• This version has no new functionality but does fix a problem with an expiration date that had inadvertently crept into the shipped program. We sincerely apologise for any inconvenience.

CrystalMaker 2.0.3

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. Installer and Updater Enhancements. The Installer is now more flexible, allowing installation of non-core components without overwriting an updated application.

3. 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.

4. 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.

5. 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.

6. 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.

7. Miscellaneous changes. This release includes a number of minor changes and bug fixes, which are listed below:

   • Automatic bond searches now correctly update site coordination numbers.
   • A problem which affected the scaling of some molecular structures stored in text files on initial input has been fixed.
   • Keyboard shortcut (accelerator) keys are handled much more reliably now; an accelerator intended for the Graphics window will be properly handled even if a palette window has the keyboard focus.
   • File Preview icons are now displayed for non-administrator users in "All Users" installations.
   • The Selection > Select > Deselect All command has been renamed: Clear Selection. Choosing this command now immediately deselects all items.
   • Auto-positioned atom labels are correctly displayed for wireframe structures.
   • Stick plots are now displayed correctly, with rounded "ball-joint" spheres.
   • The default multipliers for the Define Supercell dialog are now (2,2,2), and the structure is now properly replotted after applying changes.
   • General equivalent position data from CrystalMaker Text, STRUPLO, and CIF files are now imported and exported correctly.
   • The Plot Range palette now updates immediately and the unit cell is properly displayed following a Transform > Molecule To Crystal command.
   • Choosing the Help command from the Site Browser contextual menu now opens the Site Browser help page.
   • The image from a previous Red-Blue or Stereo Pair mode rendering no longer appears after switching back to Mono and trying to select an atom with, e.g., the Bond Distance tool.
   • The Site Browser is now updated properly after a text file has been loaded into an existing window from the Files pane.
   • The rendering of thumbnail badges for text files in the Files pane has been improved.
   • Non-administrator users running CrystalMaker in multi-user installations no longer get the 'unable to read preferences' alert every time the application is launched.
   
   

CrystalMaker 2.0.2

Released: 28 January 2008

1. 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).
   
   
2. 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.
   
   
3. 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.
   
   
4. Miscellaneous changes. This release includes a number of minor changes and bug fixes, which are listed below:
   • The Edit > Copy Graphics, File > Export > Graphics, and File > Export > Web Page commands again generate correctly-sized and clipped images.
   • Choosing the Edit > Preferences command no longer causes a crash.
   • The progress window no longer remains active indefinitely after copying or exporting large, high-resolution images.
   • In Black-and-White mode, rendered and translucent atoms no longer have coloured or random backgrounds.
   • Plain cylinder bonds are now smoothed in black-and-white mode, and bonds drawn in polyhedral plots are also smoothed when they should be.
   • Playback of structures from the Views or Files pane with rotation and fast rotation mode is now smoother.
   • The File > Take Snapshot command no longer switches the Overview pane to "Views".
   • After using the Overview window's thumbnails slider control, scrolling the mouse wheel will now scroll the thumbnails, not the slider.
   • Palette windows now retain their visibility state when switching in and out of full-screen mode.

CrystalMaker 2.0.1

Released: 14 January 2008

1. 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.
   
   
2. 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.)
   
   
3. Miscellaneous changes. A number of minor issues have also been addressed in this release:
   
   
   • A problem in generating general equivalent positions, which resulted an incorrect number of atoms and coordination values for complex spacegroups, has been fixed.
   • Atoms are now scaled properly in stereo pair plots.
   • In All Users installations, a properly-licensed application no longer asks the non-administrative user for his licence code.
   • Schoenflies symbols are now rendered correctly in the Spacegroup Browser (Windows Vista).

CrystalMaker 2.0.0

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...