These notes refer to a legacy product that is no longer supported. Please order your CrystalMaker 11 upgrade, and look forward to a new era of advanced chemical & materials modelling - plus our usual service and support!
Improved LAMMPS File Import. Some users are working with massive structures, output as "dump" files from the LAMMPS program. In order to track atoms within these massive datasets, the atom label is required. Unfortunately, CrystalMaker's 6-character label limit can mean that labels end up being truncated - especially if they have a two-character element symbol as the prefix.
In this version, CrystalMaker detects possible label overflow and will either truncate the symbol (prefix) to one character, or omit it entirely. This allows up to 1-million unique atom IDs (from 0 to 999,999).
Smart View Sorting. Earlier versions of CrystalMaker allowed sorting of views in ascending or descending order, using the view labels. This used a straightforward string comparison (e.g., "alpha" comes before "zulu"). Sorting has been made smarter in this version, taking account of numerical suffices so that numbered views are sorted in a more human-readable manner (e.g., "10" appears after "2" and not before).
Miscellaneous Changes. This version includes updated documentation, more-flexible import of atom vector data, plus a bug fix for LAMMPS file import.
Updated User's Guide, including notes on file synchronization and Apple's recent withdrawal of support for QuickTime for Windows.
When reading atom vector data ("AVEC" card) from a CrystalMaker text file, CrystalMaker no longer enforces a minimum vector length of 1.5 Å. Instead, vectors are plotted as defined by the input data, even if this means that some (extra-short) vectors will be hidden inside their host atom.
Updated View Direction when loading a CrystalMaker binary file. Some older files were saved with their view directions inverted. This is now automatically corrected when reading the files into the program.
Fixed a possible crash when reading from a LAMMPS file with long atom label strings.
Improved Vector Metrics. Atom vectors drawn in the "Through Atom" style now have a more balanced appearence. The tail of the vector is drawn slightly longer to make the overall vector appear centred on the atom.
Note that both "From" and "Through" vector styles have the same length from the atom centre to the tip of the vector cone; this is the "length" specified in the vector panel. The vector tail is a cosmetic addition.
Miscellaneous Changes. This version includes minor bug fixes for screen tools, movement of the Lattice Plane tool, rotation of selected atoms, and visualizing coordination details for massive structures via the Distances Explorer.
The Bond Angle tool now only writes output to the log when the measurement has been locked, i.e., the user has clicked for a fourth time to “finalize” the measurement. Previously, output was displayed whenever the mouse moved, which tended to fill the log.
Fixed a rare problem when dragging the Lattice Plane, which could cause the program to become unresponsive.
Rotating selected atoms in a crystal now works correctly in thermal ellipsoid mode.
The Distances Explorer again works correctly with massive structures (> 200,000 atoms).
Miscellaneous Changes. This version includes bug fixes for PDB file import.
CrystalMaker can now read from PDB files which have extended headers running to over one thousand lines.
When importing a PDB file as a crystal (rather than a molecule), CrystalMaker now correctly generates atoms in the full molecular cell range.
Refreshed Site Browser. The Site Browser has been redesigned to offer a clearer, fresher look. List row height has been increased and the background colours have been made lighter.
Automatic View Numbering. A new Rename Views Numerically command has been added to the Overview Window's Actions menu. This command will rename all View thumbnails, apply numbers in sequence. This is useful if you are working with a large animation and would prefer simple, numbered views - rather than having the original filename(s) included in view titles
Miscellaneous Changes. This version includes documentation updates and minor bug fixes for polyhedral display and the Show Molecular Cell command.
Fixed a problem with polyhedral face generation (introduced in the previous update), whereby individual faces could show fragmented views, owing to an incorrect sorting of their vertices.
Fixed a subtle issue with the Show Molecular Cell command where, for "lopsided" structures, the command could fail.
The Make Polyhedron command no longer prints diagnostic output to the Console window.
Updated online help and user's guide.
Colour Atoms by Coordination. A new Colour by Coordination contextual menu item has been added to the Site Browser (and its actions menu in the floating palette). This will apply a rainbow colour scheme to all atoms, ranging from blue (zero coordination) to red (maximum coordination). In this way, you can easily track variations in coordination number across a complex disordered system (although this may also be instructive in ordered systems too).
Miscellaneous Changes. This version includes documentation updates and minor bug fixes for polyhedral display and the Place Molecule command.
Fixed an exceedingly-rare issue with the display of polyhedra where large faces included co-linear atoms.
Fixed a memory condition with the Place Molecule command for a crystal structure.
Updated online help and user's guide.
Projected Bond Distances. The Bond Distance tool now prints the projected distance (in the plane of the screen) in the Log. This complements the displayed distance (in three-dimensions of the plot) which is also printed in the Log. This feature should be useful to electron microscopists, who have to work with structure projections in two dimensions.
Load Site Label "Properties". The CrystalMaker Text format (CMTX) now allows you to load floating-point "properties" for each crystal site or atom. Instead of entering a site label as a character string (e.g., "T1"), you can enter a floating-point number (e.g., "0.1234"). This then allows you to display this value as an atom label.
Note: You should use a floating-point number, not an integer - otherwise the file might be interpreted as a STRUPLO-format file and your "properties" will be ignored.
Miscellaneous Changes. This version includes a minor enhancement to the Relax Molecule command and a fix for reading certain CIF files.
Improved the Relax Molecule command, with more sophisticated four-body potentials.
An extremely-rare issue with reading CIF files which contain nested single quotes on the last line of the file, has been resolved.
Improvements to CIF Import. In this release we have streamlined the syntax checking for symmetry, relegating the warnings for non-standard spacegroup symbols to the Log - provided that the same input file contains a valid list of general equivalent positions (required, as part of the CIF file format, but occasionally ignored by third parties).
CrystalMaker also now correctly handles the import of Biso values, which are converted to the more-generally-used Uiso format, during thte import process.
Miscellaneous Changes. This version includes a minor enhancement to the Bend command and the addition of a command to the toolbar Range menu.
The Selection > Bend command now uses the horizontal plot centre as its reference point, rather than the three-dimensional centre-of-gravity. Whilst both methods are equally valid, the new scheme ensures that the bent lattice is centred with respect to the starting conditions.
The Show Asymmetric Unit command has been added to the window toolbar's Range popup menu.
3D Printing Support. CrystalMaker can now generate STL files - which are widely supported by 3D printers - thereby making 3D printing so much simpler, without the need to convert a COLLADA 3D file in a third-party program.
CrystalMaker uses the STL binary format, resulting in very compact files. To generate such a file, choose the new File > Export > STL 3D File menu command. .
Miscellaneous Changes. This version includes improved density output, a workaround for reporting operating system versions, fixes for the Make Polyhedron command and for CCL file import.
Improved "atom density" output. The calculation now lists both the density of sites and the density of atoms (taking into account site occupancies).
Workaround for determining the operating system version for OS X "Yosemite" and later.
Fixed an occasional crash related to the use of the Make Polyhedra command.
Spacegroup symbols which end in a digit (e.g., "I m a 2") are now correctly loaded from CCL files.
This version includes important bug fixes and compatibility enhancements and is recommended for all users.
Atom Vector Import. CrystalMaker can now read (and write) atom vectors from a CrystalMaker text file, using the new AVEC card. Users can list each vector, specifying the atom type (site label) and fractional coordinates of the atom to which the vector should be attached, the orientation of the vector, [UVW] and its length (can be left as zero), the colour and vector style.
The syntax is straighforward:
For example:
AVECHere we have three vectors on each of the atoms at {1, 0, 0}, {0, 1, 0} and {0, 0, 1} - and coloured red, green and blue, respectively. Each vector is of length 2 Å and directed along the crystallographic x, y and z axes, respectively.
Please be aware that CrystalMaker can only plot vectors which are attached to visible atoms, within the current plot range. We advise you to use the XYZR card to specify a plot range in the text file.Please see online help (CrystalMaker > Help) or "Appendix B: CrystalMaker Text Format" in the CrystalMaker User's Guide, for more details about the syntax required.
TOPAS Structure File Import. CrystalMaker can now auto-detect, and load, crystal structure input files for the TOPAS structure refinement program. CrystalMaker can read the full spacegroup, unit cell and asymmetric unit (including occupancies and optional isotropic or anisotropic displacement parameters).
Note that TOPAS structure files use the generic .str file extension - which is also claimed by a number of other programs including ATOMS and STRUPLO (also read by CrystalMaker). There is no way, therefore, for the operating system to assign a unique file icon to these files.
DMol3 Structure File Import/Export. CrsytalMaker can auto-detected and load DMol3 ".car" (single molecule) and ".arc" (simulation trajectory) data files. The latter, multi-structure files, are loaded into the same window, and represented by separate View thumbnails in the Overview window. This makes for easy synchronization and animation of extended sequences. Each structure also has its energy (where supplied) displayed in the Notebook pane.
CrystalMaker can also export structural data as a DMol3 ".car" file. Note that the format only specifies atomic coordinates - and so is useful only for molecular structures.
Improved Relax Molecule for Inorganics. In response to customer feedback, we performed some major work on the the treatment of small inorganic molecules. While we keep Universal Force Field (UFF) force constants where no MM3 are available, a number of bond lengths and angles for small inorganic molecules have been revised to their standard values (rather than simply relying on the sum of covalent radii plus a correction term). The decision-making code has updated to help apply these new bond lengths in the correct circumstances.
The update is mainly focussed on H, N and Si containing molecules, including Si and Al-containing molecules; ammonia-like compounds; H2X compounds; N in single, double, resonance and triple-bonding scenarios. Decision-making has also been updated or corrected for some potentials that had been coded in previously. Extensive testing has taken place to check geometries obtained through new minimiser.
Spaces-Aware Tile and Stack Windows Commands. Mac users with multiple screens and/or "Spaces" can now use the Window > Tile and Window > Stack commands to arrange windows neatly on the current space - without disrupting any windows on other spaces.
In previous versions of the software, these commands consolidated all CrystalMaker document windows onto the current space - which was often not the desired behaviour. Now, only windows displayed on the current space will be tiled or stacked.
New Spaces-Aware Auto-Rotate All Command. Holding down the shift key changes the Transform > Auto Rotate... command to Transform > Auto Rotate All (or Stop Rotating All if the frontmost window is already auto-rotating). This allows one to easily start (or stop) rotating all windows in the current space.
For clarity, the other dynamical Auto Rotate (no ellipsis) menu option has been removed (this simply duplicated the function of the toolbar’s Auto Rotate button).
Note that holding down the shift key whilst clicking the window toolbar’s Auto Rotate button has the same behaviour as clicking the equivalent menu command.
Miscellaneous Changes. This version includes miscellaneous enhancements, bug fixes and system workarounds.
The Add Hydrogens command will now recognise boron and add the requisite number of H atoms.
Updated User's Guide. This documents the new features and includes a far-more detailed table of contents.
More robust error-checking when loading binary files which might contain invalid atom IDs, owing to an issue with an earlier version of the software.
Fixed a bug with undo levels being unavailable if a structure in another window is auto rotating.
Two-finger trackpad clicks are now correctly recognised as "right-mouse" clicks. (This problem was unique to OS X 10.10 "Yosemite".)
Resolved an occasional problem with COLLADA 3D files appearing blank when displayed in the "Preview" application (the same files were rendered correctly in other 3D applications).
COLLADA 3D iBooks/Yosemite Workaround. We have devised a workaround for an issue with the latest version of "iBooks Author" running on OS X 10.10 "Yosemite". An error in iBooks Author meant that some COLLADA 3D files (which previewed correctly in the Finder and Preview.app) were not rendered in iBooks Author.
Although we discussed the problem with Apple, it became clear that the timescale for fixing the issue at their end was longer than we would have liked, and we therefore decided to take our own action. We have changed the way in which the initial model view is presented, using a clearer representation which seems to work with the current iBooks Author running on both OS X 10.10 "Yosemite", as well as earlier versions fo the operating system.
Improved COLLADA 3D Export. In addition to the iBooks Author-specific changes, we have streamlined the COLLADA 3D export, removing the lighting options sheet (CrystalMaker's rendered lighting is automatically applied, in place of the crude default COLLADA "head on" lighting). Exported models are now automatically centred: this will help users who wish to print models by loading them into the free "Blender" program for conversion to proprietary printer formats.
Miscellaneous Changes. This version includes miscellaneous bug fixes and system workarounds.
Fixed an issue with atoms appearing too small when switching from a stereo-pair plot back to "mono" mode.
Atom vectors are now retained when the plot range is expanded.
Atom vectors are again read correctly from a binary file.
Fixed a rare issue in which the program could crash when reading from a saved crystal binary file.
Fixed a rare crash relating to display sleep - a workaround for a system memory issue.
Smoother Multi-Touch. Trackpad-controlled Rotation and Magnification gestures are now much smoother and take into account the time required to replot the structure.
Measure Bonds. A new Measure > Bonds command provides a listing of all the visible bonds in the current structure, including atom information, bond lengths and the total number of bonds. The total number of bonds is also listed (in the Log) when choosing the Measure > Chemical Formula command.
Robust Relax Molecule. A number of improvements have been made to the Relax Molecule command to cope with possible system memory issues, and to provide a workaround for a system bug with display sleep.
The relaxation will now automatically stop if it detects a low-memory condition. This prevents a subsequent crash, and preserves the current state of the relaxation.
We have discovered an apparent system bug associated with display sleep. Memory requirements dramatically increase, as it appears that video and other memory is not being correctly purged by the system. To mitigate the effects of this bug, CrystalMaker now looks out for display sleep/wake events and takes appropriate action, suppressing screen updates as necessary.
Miscellaneous Changes. This version includes performance improvements and miscellaneous bug fixes.
The Set Range command is now considerably faster.
The Crystal Editor now prevents invalid rhombohedral angles (≥ 120°) being applied.
Crystal and molecule binary files saved by recent Windows versions and including single-character element symbols can now be correctly read.
Fixed a rare "Error generating atom spheres" error that could occur when attempting to transform the unit cell by projecting onto a lattice plane.
The Make Polyhedron command now correctly adds any new sites to the zeroth unit cell.
Fixed a memory issue with the Relax Molecule command.
Redesigned Symmetry Options. The Symmetry Options dialog (accessed from the Crystal Editor) is now resizable vertically, making it possible to see a complete list of General Equivalent Positions (GEPs) for all spacegroups. The list now features slimline "+" and "-" buttons as well as a status bar. Clicking anywhere in the list activates the Customize option. Multiple selection is now possible (via dragging or command- or shift-clicking) which allows for the removal of multiple GEPs in one step.
Miscellaneous Changes. This version includes improved documentation and miscellaneous bug fixes.
Minor updates to Online Help, User's Guide and the Tutorial.
The File > Import commands for LAMMPS and GROMACS now work correctly.
Fixed a rare failure in the new Show > Nearest Neighbours command.
The One Cell button in the Plot Range window now functions correctly.
Tabbing between columns the GEPs list of the Symmetry Options window now works correctly .
"Grow" Atoms and Bonds to Repair Broken Bonding/Molecules. Atoms with incomplete bonding can now have their coordination repaired, making nearest-neighbour atoms and their bonds visible. Similarly, "broken" molecules can be repaired. In both cases, missing atoms and bonds are caused by plot range truncation. Two new menu command, Selection > Show > Nearest Neighbours, and Selection > Show > Entire Molecule, will intelligently expand the plot range in the appropriate directions, to "grow" the selection, whilst keeping the rest of the structure the same.
Show Asymmetric Unit. CrystalMaker now makes it even easier to isolate single molecules in a molecular crystal. A new menu command (Transform > Optimize Range > Show Asymmetric Unit, keyboard shortcut: command-shift-U) will display the original asymmetric unit (as loaded from a raw text file). For most molecular crystals, this will correspond to one or more intact molecules.
This new command complements the existing Show Molecular Cell command, which displays the complete contents of one unit cell, optimized to ensure that all molecules are intact.
Please note that the Show Asymmetric Unit command will take an existing structure and show the asymmetric unit. If the fractional coordinates of the asymmetric unit have been changed (e.g., earlier versions of CrystalMaker automatically wrapped the asymmetric unit sites into the same unit cell), then the results may be unpredictable, and some molecules may appear broken.
Add Hydrogens. CrystalMaker can now automatically add hydrogen atoms to any molecule. The program assumes that the structure needs to be fully saturated and performs a relaxation on the new hydrogens to yield an optimum geometry (the positions of pre-existing atoms are not relaxed, thereby making this command suitable for adding hydrogen atoms to molecular structures refined using X-ray data).
The hydrogen positions should refine quickly - but if you wish to stop the relaxation, you can do this in the normal way, by clicking the Stop Relaxing button in the window toolbar, or by choosing the same command from the Transform menu.
Note: if you require double or triple bonds (e.g., taking a C—O unit and adding hydrogens to make H2C=O instead of H3C—OH), you may need to delete some of the newly-added hydrogen atoms.
Relax Selection. It is now possible to relax part of a structure, (e.g., a side-chain of a molecule, or atoms on a surface), instead of the entire structure. One simply needs to select the atoms to be relaxed, and click the Relax button in the window toolbar (or choose: Transform > Relax Selection).
New "Make Polyhedron" Bonding Option. The Make Polyhedron command has been improved with a new, default, bonding option that generates appropriate global bond specifications, based on the selected distance range. As a result, polyhedra will be preserved as your plot range changes, and most users will find this more intuitive than the older default option, which was to generate only symmetry-related bonds for the current plot range.
The Make Polyhedron window has been redesigned to include the new default bonding option (together with the older options). Descriptions have been added to clarify the various choices.
One-Click Atom & Bond Addition. It is now possible to define a complete molecule - with all atoms and chemical bonds - using just the Add Atom tool. Simply hold down the shift key as you click; a bond will be added between the new atom, and the previously-added one. To change the "anchor point" for a new bond, click on an existing atom with the Add Atom tool. The clicked atom becomes highlighted, indicating that any new bond will be extended to this atom.
For example, using the Add Atom tool, you could create a methane molecule, CH4 (5 atoms and 4 bonds) in the following steps:
Choose C from the Atom Picker.
Click in the Graphics pane to add the C atom. Note that this is shown highlighted, ready for bonding.
Choose H from the Atom Picker.
Hold down the shift key and click in the Graphics pane. A new H atom appears, bonded to the original highlighted C atom. The new H atom is highlighted.
Click to add your second H atom. This will be shown highlighted.
Hold down the shift key and click on the C atom. A bond is added between the second H atom and the C atom, and the C atom is once again highlighted.
Hold down the shift key and click to add a third H atom and a bond to the C atom, in the same step.
Click to add a fourth H atom. Again, this latest atom will be shown highlighted.
Hold down the shift key and click on the C atom to bond this to the fourth (and highlighted) H atom.
Note that, for more extended molecules, you may wish to shift- click between C atoms to define a backbone, then use the new Add Hydrogens command.
Two New File Formats Supported. CrystalMaker can now import crystal structure files generated by two popular energy modelling programs: LAMMPS program (Sandia National Labs) and GROMACS. These formats can be auto-detected, so users can drag-and-drop data files into the program for instant display. As with other file formats, CrystalMaker supports multi-structure files, displaying individual structures as thumbnails in the Views pane of the Overview window.
Rotate Selection in a Crystal. As part of our new crystal-engineering tools, it is now possible to rotate a selected group of atoms - in "crystal" mode (previously this was limited to "molecule" mode). To rotate a selection, you must click the Rotate Selection button in the bottom right-hand corner of the Tools palette.)
Select Symmetry-Related Atoms. You can now quickly select all atoms that are related by symmetry in your crystal. Simply select one atom, and choose the new: Selection > Select > Symmetry-Related Atoms menu command. All symmetry-equivalent atoms (i.e., those with the same site in the asymmetric unit) are shown selected.
Smart Range Extension. CrystalMaker 9 now caches atom attributes before changing the plot range, so that custom atom colouring, styles, labelling, etc., will be preserved after a range change. (Earlier versions of the software could reset custom atoms when the plot range was changed.)
Miscellaneous Changes. This version includes an improved Plot Range window, new keyboard shoftcuts plus miscellaneous bug fixes:
The Plot Range window now reports all ranges using positive fractional coordinates. This ensures that displayed values, as measured on screen (e.g., using the Atom Info tips) are reflected in the Range window.
(Note that it is still possible to enter negative fractional coordinates, but these will be converted to positive values, as required by CrystalMaker's unit cell generation engine.)
New keyboard shortcuts have been added, as follows:
| Show Asymmetric Unit: | cmd - shift - U | |
| Define Cluster: | cmd - option - K | |
| Edit Bonding: | cmd - option - B | |
| Make Polyhedron: | cmd - shift - M |
The delay before showing an Atom Info Tip has been increased from 1 to 1.5 s.
The Relax Molecule command now issues a warning when any atoms are hidden.
Oxygen double bonds are now correctly identified by the Relax Molecule command.
Attempting to add hydrogens to a fully-saturated molecule no longer results in a phantom hydrogen atom being listed in the Site Browser.
When adding new atoms to an existing molecule using the Add Atom tool, the atoms are correctly positioned in the vertical plane.
Depth Fading now works correctly when building a new molecule with the Add Atom tool.
Fixed a bug with the colouring of photo-rendered thermal ellipsoids.
Editing thermal ellipsoid types using popup menus in the Crystal Editor now works correctly.
Thermal ellipsoids are now correctly drawn as small spheres, when specified.
New User's Guide. The brand new, 10th edition of the CrystalMaker User's Guide is now complete, and is included with this version under the Help menu.
This new edition covers all the new features in version 9, with a new layout and many more illustrations. This edition is optimized for viewing in two-page format.
Miscellaneous Changes. This version includes a new application icon, improved Place Molecule behaviour, plus miscellaneous bug fixes..
Improved application icon. CrystalMaker 9 sports a higher-resolution application icon with some subtle highlights.
The online help system has been reorganised to match the CrystalMaker User's Guide. A new section on "Manipulation" has been included.
The Place Molecule command now prompts the user to discard symmetry, before placing a molecule into a crystal structure.
This version now correctly auto scales structures on loading from a text file.
The Crystal Editor now shows site occupancies that are greater than one.
VASP files with non-orthogonal crystallographic axes, but with coordinates defined relative to orthogonal axes, are now correctly plotted.
A rare issue relating to rhombohedral lattices in the Transform Cell command has been resolved.
Thermal ellipsoids defined with the "blank" style are now correctly hidden, and not drawn as black (or white) circles, as before.
Improved Copy Graphics Command. CrystalMaker now copies graphics to the clipboard in the TIFF format, instead of the old PICT format that has been used for the past 20 years. This is a workaround to fix a problem with many third-party programs (including Pages 5) which are unable/unwilling to work with the PICT format. CrystalMaker also displays a new Copy Graphics sheet, which makes it easier to scale the output size, in relation to the existing screen image.
Please note that, because of the lack of support for PICT graphics, we no longer allow PICT vector images to be copied to the clipboard. However, these can still be saved in a graphics file, via the File > Export > Vector Graphics command.
Automatic Pen Scaling. When copying or exporting graphics, CrystalMaker now automatically scales pen widths (as used in bond lines, polyhedral edges and atom frames). This should help ensure that output better matches the screen display.
As part of this change, the Scale Pen Widths checkboxes have been removed the Atoms and Bonds Inspectors.
(For fine-scale control of line widths, users can resize the Graphics Window: making the window larger will reduce line widths in copied or exported graphics, whereas making the window smaller will increase line widths in copied or exported graphics.)
Miscellaneous Changes. This version includes Leap Motion status, improvements to the Add/Delete Bond tool, and a less verbose Relax Molecule command.
If a Leap Motion Controller has been installed, the program displays a status message at startup.
The Add/Delete Bond tool now correctly highlights a sphere when it is clicked.
The Add/Delete Bond tool no longer allows self bonding (e.g., by clicking repeatedly on the same atom).
Less-verbose Relax Molecule command. Less information is now printed in the Log during the course of the relaxation.
Leap Motion Control. You can now rotate and scale your structure using simple hand gestures, and a Leap Motion controller.
Improved Relax Molecule Tool. The molecular relaxation tool can now cope with unusual molecules such as the square-planar PtCl4, and molecules with a see-saw geometry. Specifically, the algorithm now auto-detects the presence of S, Se or Te bonded to four halogens, and applies the correct bond angles and/or distances.
Miscellaneous Changes. This version includes improved online help and faster rotation.
New help links for each of the Overview window panes.
The new command-arrow 90° rotation shortcuts now only apply if the graphics pane is active. This then allows use of these shortcuts when editing text in the Notes pane, or the Log pane of the Overview window.
Rotating using a mouse wheel, or via a two-finger slide on the trackpad, is now much faster in "Fast Rotation" mode.
New Rotate Submenu. New commands, added to the Transform menu, allow easy rotation of the model through 90° left, right, up or down. Keyboard shortcuts (cmd ←, cmd →, cmd ↑, cmd ↓) facilitate rotation. (Note that these new commands supplement the existing Rotator Controls on the Tools palette, which allow the user to specify a precise angle.)
Faster multi-touch rotation and scaling. Using the trackpad to control rotation and scaling is now far more responsive in "Fast Rotation Mode".
Miscellaneous Changes. This version includes a few, minor, bug fixes, plus an improved method for licensing verification, designed to assign our Department or Campus licence holders.
Fixed a missing-icon issue with the "Site Browser" window toolbar button.
Fixed an issue with the Labels Inspector. Toggling the Scale labels with structure checkbox now immediately applies the change to the current structure.
Improving licensing search for Department and Campus licences, makes it easier for IT personnel to install the software for multiple users on the same machine. (Personnel should contact us directly for instructions.)
After more than six years of continuous support and over 40 free updates to CrystalMaker 8, it's now time to move on. We're delighted to announce CrystalMaker 9.0: presenting a new dimension to crystal and molecular structures, with advanced energy modelling and crystal engineering tools - plus a myriad of great new features, many suggested by users like you. Thanks for your past support, and we look forward to welcoming you as new users of CrystalMaker 9...
Energy Modelling. Energy modelling is now built into CrystalMaker, via the new Transform > Relax Molecule command. The software uses a sophisticated Monte Carlo algorithm to progressively relax a bonded structure. Organic chemists will be pleased to discover that this algorithm can auto-detect carbon hybridisation (e.g, sp2 and sp3), which makes molecular optimization much easier.
CrystalMaker uses multi-threading to ensure that the program remains as responsive as possible during the refinement process - and to take advantage of multiple processors on your system. The structure is updated at each stage, and can continue to be rotated during the refinement process. Use the Transform > Stop Relaxing Molecule command to cancel the refinement at any time.
Molecule Builder. A new "Add Atom" tool has been added to the Tools palette. This lets users start with a blank canvas (an empty window) and design new structures, simply by choosing atom species from an Atom Picker Palette, and clicking in the Graphics pane. Use this, in conjunction with the energy minimization, to produce realistic molecular structures.
The Atom Picker provides a number of preset atom types (e.g., "organics", "silicates", "halides") which can be used to populate the palettes buttons. You can customize the palette by adding your favourite elements: click and hold any button and choose a new element from the popup menu that appears.
Crystal Engineering. CrystalMaker now makes it easier to convert molecular structures into crystals, with far greater flexibility in tiling and positioning. We also now provide atom-level manipulation for crystal structures, including the ability to place molecules, insert new atoms, add (or remove) space, duplicate atoms, edit their coordinates and change their types:-
Flexible Molecule-to-Crystal Conversion. Extended, improved Molecule-to-Crystal command provides much greater flexibility with the freedom to control your lattice parameters, tile/wrap atoms and molecule placement. This should prove very welcome to modellers!
Insert Space in the Unit Cell. A New Lattice Plane > Insert Space command, for crystals. This lets you insert an oriented block of space inside the crystal lattice, using the Lattice Plane to define the orientation and position of the block. Your unit cell will then be recalculated to show the space that you request. You can use this space (which can be removed, by specifying a negative distance) to insert new blocks of atoms - e.g., to create intercalated compounds, pillared clays, etc.
Place Molecules inside Crystals. Thanks to popular demand, the Place Molecule command works for crystals, allowing you to insert blocks of atoms, small molecules, interfaces, - or whatever you fancy - inside an existing crystal structure.
Place New Atoms Inside a Crystal. Use the new Add Atom tool to insert new atoms inside an existing crystal structure. CrystalMaker automatically applies lattice translations to your newly-added atoms, thereby preserving the three-dimensional periodicity of the structure.
Duplicate Atoms inside a Crystal. You can now duplicate one or more selected atoms inside a crystal structure (as well as just a molecular structure), using the Selection > Duplicate command.
Directly Edit Atoms in a Crystal. You can now edit atomic coordinates and change their types without having to re-generate an entire crystal structure. Simply select the atom(s) you wish to edit and choose one of the following commands:
Selection > Atoms > Change Atom Type
Selection > Atoms > Edit Coordinates
Move Atoms Inside a Crystal. Atoms can be (permanently) moved in a crystal lattice, simply by clicking-and-dragging them with the Arrow tool. (Previously, the program gave the appearance of doing this, but the atoms soon reverted to their original positions, as soon as the structure was recalculated.
Please note that any crystal-engineering changes you make will result in the spacegroup symmetry being reduced to P 1. You will be prompted to agree to this, before any such change is imposed.
Nanotube Creator. You can easily build your own carbon nanotubes using our new Selection > Bend command! This prompts you to specify a radius of curvature - or accept the program's calculated value (designed to generate a cylinder). The selected structure is then bent around an imaginary cylinder with that radius. The command can be repeated around a second axis to make a curved surface with a spherical section.
For example, to make a carbon nanotube, one would start with a sheet of graphite (see examples in the Crystal Structures Library), oriented "side on", and with all atoms selected.
Distances Explorer. The new Measure > Explore Distances command provides a colourful histogram display of nearest-neighbour distances between the selected atom-pairs.
The Explorer window can be customized, on the fly, to show detailed coordination data for your entire structure, reminiscent of a pair-distribution function. A slider gives real-time control over the histogram "bin" size, and you can choose multiple search criteria, as well as the overall distance range.
An optional Table view displays detailed output, and both data and graphics can be exported.
Collada 3D Export (for iBooks). Users can now generate standalone 3D models using the COLLADA file format - as used in Apple's iBooks applications for Mac and iPad - via a new File > Export > COLLADA 3D File command. The resulting models, which feature very-high quality photo-realistic rendering, allow full rotation and scaling, can be viewed by a wide-range of 3D rendering programs, some of which provide support for conversion to other 3D formats.
Mac users can view fully-rotatable CrystalMaker models on their iPads by simply dragging CrystalMaker-generated COLLADA (".dae") files into the iBooks Author application (a free download from the Mac App Store), and pressing the Preview button in that application's toolbar.
Interactive Measurement. New screen tools provide real-time display as the mouse is moved, including coordination details, bond, angle and torsion angles display. Core Graphics (Mac) provides clearer, rotated text, and smooth outlines.
Information Rollovers. The Bond Distance and Angle tools provide live feedback as you move the mouse. You can anchor either tool, and explore distance/angles to any other atom in the displayed structure.
Smart Bond/Torsion Angle Tool. We have merged the functionality of the former Torsion Angle tool into the Bond Angle tool. You can now measure regular bond angles and torsion angles with the same tool, and show more detailed information on screen.
Smart Arrow Tool. We have merged the former Atom Info tool into the Arrow tool. As you move the arrow tool over your structure, atoms are highlighted and their interatomic distances shown.
Atom Info Tips. As an option, you can choose to identify each highlighted atom under the Arrow tool, with a special "Atom Info Tip". This "overlay window" identifies the site, its occupancy, and atom number. Clicking anywhere on the tip expands it, to reveal detailed information about the highlighted atom's coordinates, bonding, coordination state, etc. Buttons are included to print Site, Bonding and Angle information in the Log.
Click anywhere in the expanded tip to collapse it. To hide the tip, simply move the mouse away from the highlighted atom. Note: if you find the Info Tips intrusive, they can be turned off via the Measure > Hide Atom Info Tips command.
Model Inspector. You can now control your model’s display and rendering settings in real time, using the new Model Inspector. This floating palette incorporates elements of the old "Model Options" and "Rendering Options" palettes, adding new slider and arrow controls, background presets - and "live" operation: a major productivity boost.
The Model Inspector is divided into seven panes, denoted by small buttons at the top:
Atoms - showing all sites in your structure, grouped by chemical element, with their sphere, ellipsoid and polyhedral styles - plus controls to adjust sphere and ellipsoid sizes.
Bonds - all global bond specifications defined for your structure, with additional controls for setting cylinder radii.
Unit Cell & Surface - Lets you edit your unit cell display (for a crystal structure), including the frame style and colour; plus toggle a surface overlay, control its style and colouring.
Labels - Change the label content, positioning and font. Toggle labelling on or off.
Background - Includes handy presets for one-click setting of your window's plain or gradient-fill background.
Reflectance - Control the rendering of spheres, bonds, polyhedra and the surface overlay. You can also adjust the illumination direction and its intensity.
Depth - Lets you accentuate the three-dimensional appearance of your structure by controlling perspective, depth fading (with live Depth Zoom slider), and actual 3D display: red/blue stereo or stereo-pair plot.
Multi-Touch (Mac). Following popular request, we have provided "multi-touch" support for our Mac users. Use the trackpad to scale your structure with the "pinch" command. Rotate your structure (about the screen’s Z axis) using the "rotate" gesture
Combined Demo Version. CrystalMaker now behaves in the same way as our other software products, with a single, universal application for Demo, Full and Updates. This will make it much easier to obtain the latest version of the software, without having to retain an original installer file (although we recommend that you keep backups of the software!). CrystalMaker launches in "Demo Mode", and can be unlocked, via a licence code.
Miscellaneous Changes. This version includes a myriad of smaller changes, some of which will provide a major boost to your productivity:
Streamlined menus make it easier to find important commands. All measurement-related commands have been moved from the Transform menu to a new Measure menu. The Rendering menu has been merged into the Model menu. The Window menu has been improved, and the old Workspace submenu removed, replaced by a single Reset Workspace command.
New Empty Molecule command (cmd-shift-N) lets you create a new, blank window. This can serve as a drag-target, for dropping any text or binary file into; or you can use the blank window as a canvas to design (and relax) a new molecular structure, using the new Add Atom tool, in combination with the existing Add/Delete Bond tool.
Streamlined Tools palette. The old Info, Annotation and Torsion Angle tools have been removed. Their functionality has been merged into the Arrow tool, Annotation window toolbar button, and Bond Angle tool, respectively.
Bonds can now be selected by clicking on them with the Arrow tool.
Redesigned Window Toolbar layout. Includes new buttons for the Annotation popup, Relax Molecule and Model Inspector.
Column View Site Browser for the Define Cluster command: provides easier site access, especially for massive structures.
Edit > Bonding sheet now provides real-time coordination previews, as you add or edit bond specification. It also includes an Explore Distances button, letting you evaluate distance information graphically (via colourful histograms), before committing yourself to particular bond specifications.
Improved cursors for many screen tools.
Faster startup time: the "Splash Screen" has been eliminated, resulting in near-instant program startup.
Seamless auto-rotation. Individual windows can now be viewed in Auto Rotation mode, using the new Window toolbar button, or using the "Auto Rotate" dialog. Operations can continue whilst the structure is rotating, e.g., changing the model type, range and other options.
Spacegroup detection when importing text files. CrystalMaker can now "reconstruct" a spacegroup symbol from an imported list of general equivalent positions (GEPs). This means that we can reliably display spacegroup information from CIF files, using the unambiguous GEPs contained in the file, and ignoring any potentially troublesome spacegroup symbols.
Improved Discard Symmetry command - built into many of the new crystal engineering tools. Existing atom visibility and selection status is now maintained.
Batch graphics export. Lets users generate graphics files for the entire contents of the Views or Favourites panes of the Overview window.
Unicode text output to the Log pane, provides Ångstrøm symbol and superscripts (Mac).
Improved thermal ellipsoid display. The "Hollow Octant" and "Hollow Equatorial Octant" styles now use the atom colour for their lines, and feature an "ORTEP-style" hatch-shaded cutouts.
Removed the old Greyscale and Black-and-White rendering modes. Users still have the option of using simple, stylized model elements, e.g., the black-and-white styles in the Atoms pane in the Model Inspector.
Dramatic new "stereo standout", allowing much greater control with extended "out-of-the-screen" effects. (The slider control provides a safe range; use the new text control to enter values out to ±100 pixels, for really-dramatic visual effects).
Redesigned Crystal & Molecule editors with site occupancy formulae, automatic labelling feature, plus easy control over thermal ellipsoid data.
Combined Demo/Examples files provided with the program. These appear, by default, in the Favourites pane of the Overview window. They can be removed and added later, via the new Load Examples Files command in the Overview Actions menu.
New, version-9 binary file format for crystals and molecules. CrystalMaker 9 uses a new file format which is not backwards-compatible with older versions of CrystalMaker. However, the program can still read from older files generated by CrystalMaker versions 2 through 8. In addition, our existing SingleCrystal 2 and CrystalDiffract 6 programs will be updated to add support for the new version-9 file format.
New online help system, with sidebar for easier navigation. Includes expandable help topics for greater ease of use.
New system requirements: CrystalMaker now requires OS X 10.6 "Snow Leopard" or later, running on an Intel-based Mac. We're sorry, but we are no longer able to provide support for older, PowerPC-based Macs.
New Software Licensing Agreement, courtesy of our Legal Eagles at Penningtons Manches LLP.