Before (top) and after (below) using the Relax Molecule command. The lower image has been rotated slightly to show all the hydrogen positions.
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.
Multi-threading is used to improve responsiveness, provide live updates and allow the structure to be rotated during the relaxation process.
For complex molecules, you can opt to perform a relaxation on only part of the structure, by selecting it, and choosing the new Relax Selection command.
A new Add Hydrogens command will saturate an existing molecule, adding hydrogen atoms and relaxing their positions to give an optimum geometry (without affecting the rest of the molecule). This command is ideal for X-ray structures which are typically refined without H positions.
The Atom Picker, which lets you choose which atom to add to your structure.
A new Add Atom tool has been added to the Tools palette. This lets you start with a blank canvas (an empty window) and design new structures, simply by choosing atom species from an Atom Picker palette (which can be readily customized), and clicking in the Graphics pane.
Shift-clicking with the Add Atom tool lets you simultaneously add a new atom and a bond. Clicking on an existing atom highlights it, allowing you to extend bonding to a side chain or a new neighbour.
Once you have built your basic (two-dimensional) molecule, use the new Relax Molecule command to optimize it.
A multi-layer torus created using the new Bend command.
You can design your own nano-structures by bending sheets of graphite - or any other material. CrystalMaker's new Bend command lets you automatically turn a sheet into a cylinder - or you can define your own radius of curvature and simply bend the structure.
Combining sheet rotation with the Bend command results in a helical material. Repeating the command with rotation about a second axis lets you generate a curved suface with a spherical section. The possibilites are endless.
Before (left) and after (right) using the new Insert Space command to open up space inside a crystal structure.
CrystalMaker 9 offers far greater flexibility to convert a molecular unit to a crystal: with the freedom to control your lattice parameters, tile/wrap atoms and molecule placement
Make room in your crystal lattice for new blocks of atoms, and design intercalated materials, pillared clays, etc. Simply use the Lattice Plane to define the orientation and position of your insertion, then specify the width of the block to be inserted. CrystalMaker does the rest - and all without leaving "crystal" mode.
Insert blocks of atoms, small molecules, interfaces, - or whatever you fancy - inside an existing crystal structure. You can also select groups of atoms and duplicate them directly.
You can now edit atomic coordinates and change their types without having to re-generate an entire crystal structure. You can also select atoms, move and rotate them - CrystalMaker will automatically apply lattice periodicity for you.
Before (left) and after (right) using the new Show > Nearest Neighbours command to repair a selected coordination environment.
Atoms with incomplete bonding can now have their coordination repaired, making nearest-neighbour atoms and bonds visible. Similarly, “broken” molecules can be repaired in a single step.
Isolate single molecules in a molecular crystal with a new Show Asymmetric Unit menu command.
CrystalMaker now saves existing atom attributes—colours, styles, labelling— when the plot range is extended and new blocks of lattice are generated.
You can now quickly select all atoms that are related by symmetry in your crystal. This also provides a way to isolate symmetry-related bonding.
Large cavities in a zeolite structure, visualized with the new default Make Polyhedron command.
CrystalMaker can already auto-generate coordination polyhedra, but what happens if you want to visualize a void, a large cavity, or an empty "cage" structure?
Beginning with CrystalMaker 9.1, the Make Polyhedron command has a new, default, bonding option that intelligently generates bonding based on an atom selection - for example, atoms around a cavity. Polyhedra will be preserved as your plot range changes.
The Make Polyhedron window has been redesigned to make it easier for you to choose the best polyhedral generation choice, including the options of radial distance criteria or symmetry-related bonds.
The Distance Explorer palette, showing a visualization of interatomic distances for a complex silicate mineral.
The new Distances Explorer provides the most graphical visualization of coordination states in your material - and can be accessed from the Bonds editor, to provide the best-possible guide to the interatomic distances in your structure.
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.
Your histogram display can be copied or saved to disc as a graphics file. An optional Table view displays detailed output, and both can be exported as a text file.
A page from an iBook, showing embedded COLLADA 3D models.
Print your structures on a 3D printer, using CrystalMaker's new STL 3D File export option to generate a self-contained 3D printer file from the displayed structure.
Generate standalone 3D models using the COLLADA 3D interchange file format: ideal for sharing your 3D models with other applications - or for standalone visualization on your Mac (COLLADA ".dae" files are supported by OS X Mavericks and later, and can be manipulated in Preview).
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.
iBooks is a revolutionary way of teaching: it avoids many of the limitations of "chaotic" hyperlink-driven web-based learning, providing a cohesive layout in which interactive elements (of which COLLADA 3D objects are one part) are annotated and tightly bound to the educational context.
Atom info tips shown in collapsed state (left) and expanded state (right).
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.
As you move the arrow tool over your structure, atoms and bonds are labelled and highlighted. Optional Atom Info Tips help identify sites and can be expanded to reveal coordinates, bonding data, coordination states - with controls to print detailed data in the Log.
The new Model Inspector, showing background controls.
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.
CrystalMaker's new menu structure makes it easier to find the commands you need, and includes a new Measure menu, a sleeker Transform menu, and a more powerful Model menu.
The floating Tools palette is now more efficient, with fewer, but more powerful, tool buttons. We've focused on smart tools that provide rollovers and greater feedback.
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
Mac users can also use a Leap Motion Controller to rotate and scale, using simple hand gestures in space. This works particularly well using the "out-of-screen" red/blue stereo mode, giving the illusion of turning a structure between one's hands.
"ORTEP-style" colour thermal ellipsoids.
CrystalMaker 9 can import five new file formats: DMol3 ".car" and ".arc" files, LAMMPS, GROMACS and TOPAS structure files. These formats are auto-detected, so users can drag-and-drop data files into the program for instant display - and animation of multi-structure files. CrystalMaker can also now export DMol3 ".car" files.
CrystalMaker can now read (and write) atom vectors from a CrystalMaker text file. Users can specify each vector, with its host atom, orientation, colour, style and length. The simple syntax makes this ideal for visualizing "vector fields", read from energy modelling programs.
We've made it easier for you to access the software. CrystalMaker is now provided as a single executable that you can download from this site. The software initially runs in Demonstration Mode until unlocked with a licensing code. No updater is required: just download the application again.
Create new "empty molecules", and start building your new structures using the Add Atom and Add Bond tools - in combination with the Relax command.
A new Auto Rotation mode, lets you individually control rotation, spinning a structure in one window, whilst continuing to work with a structure in a different window. Operations can continue whilst the structure is rotating, e.g., changing the model type, range and other options.
Need to generate a sequence of graphics? No problem: just load the files you need into the Views or Favourites pane, and use the Overview window's Actions menu to generate a batch of graphics, one for each file.
Mac users can now work with multiple windows spread across multiple displays (or "spaces"), organising your windows by space - with the new Window > Tile and Window > Stack commands acting on the current space and not disrupting your window layouts in other spaces.
Generate simple, stylized thermal ellipsoids - in colour - with hatch-shaded octant cutouts.
The new Model Inspector allows far greater control of Red/Blue stereo, with impressive "stereo standout", resulting in a genuine illusion of molecules floating in front of the monitor..
Happy 21st! CrystalMaker 9 builds on over 20 years research and development. Find out what was new in the previous release, CrystalMaker 8.