CrystalMaker
Transcription
CrystalMaker
CrystalMaker Product Overview November 2010 New CrystalMaker 8.3 for Mac CrystalMaker 2.3 for Windows Product Overview CrystalMaker Contents Page 3 CrystalMaker The CrystalMaker Advantage What’s New in CrystalMaker Page 8 A Seamless Workflow Automatic Detection of File Formats Support for multi-structure text files Flexible interface for single and multi-structure working Animated Views with movie output Wide-ranging data export options Video recording Automatic generation of QTVR objects Outstanding, high-resolution graphics export Page 13 Outstanding Display Easy structure building Built-in model types Customizable model options Element colours and radius tables Bond and polyhedra generation Molecular crystal tools Customizable rendering options Depth profiling for massive/dense structures Page 17 Fully-Interactive Extensive range of screen tools Instantly hide/show groups of atoms Molecule–Crystal conversion Place different structures into same model Easy surface/slab creation Supercell generation Page 20 Operating System Integration Mac System Integration Windows System Integration Page 24 Diffraction Support CrystalDiffract Features SingleCrystal Features Page 29 Resources Page 30 Technical Specifications This overview covers both CrystalMaker for Mac (version 8.3) and CrystalMaker for Windows (version 2.3). Whilst the majority of the screenshots are for the Mac version, both programs share the same feature set, albeit with different interfaces, tuned for their respective operating systems. 2 Product Overview CrystalMaker 3 CrystalMaker Interactive Crystal Structures Visualization CrystalMaker is a program for building, displaying and manipulating all kinds of crystal and molecular structures. Featuring spectacular photo-realistic graphics and breathtaking 3D visualization, CrystalMaker excels at publication-quality graphics, without sacrificing ease-of-use. The program has been designed around a clean and elegant user interface that’s both visually engaging, and easy to use. Screen tools provide real-time structure rotation, scaling, selection and measurement, whilst the Overview window lets you browse multiple structures, keep track of your undo states, or assemble multi-frame animations. CrystalMaker is your vehicle for exploration and discovery in the crystalline world Whatever your area of science, CrystalMaker will engage your attention and excite your imagination. Product Overview CrystalMaker 4 The CrystalMaker Advantage A Seamless Workflow CrystalMaker can automatically detect and load datafiles from the world’s major databases, plus key formats such as CIF, Chem3D, GSAS and SHELX. CrystalMaker also provides its own, easy-to-use text format, which is ideal when you want to automate data handling. As easy as drag-and-drop Just drag-and-drop any supported data files into CrystalMaker for immediate display in the Files pane or Graphics window. The seamless data loading is matched by powerful data export: ideal for sharing data with coworkers, or running the software in parallel with simulation programs. If you need to build your own structure from scratch, you can do this right in the program, with easy-to-use crystal and molecule data editors, built-in spacegroup and symmetry handling, and automatic bond/polyhedra generation. Ball-and-stick, space-filling, wire-frame, stick, polyhedral and thermal-ellipsoid models are immediately available—and can be extensively customized. It’s in black and white As an alternative to photo-realistic graphics, stylized “line art” graphics provide ideal output for figures in many journals. CrystalMaker’s unique user interface lets you transcend static structures and work with dynamical properties: browsing multiple structures or views in the same window, animating phase transitions or chemical reactions, with the option of fullscreen viewing and automatic movie output. A new Synchronize command lets you achieve consistent results across multiple structures. Outstanding Display CrystalMaker features photo-realistic graphics with depth fading, perspective and extensive control over rendering settings. Enjoy spectacular “out-of-screen” 3D stereo, using the supplied red/blue stereo glasses. Simpler “line art” model styles— ideal for technical publications—are also available. High-resolution graphics can be exported, at user-defined size/resolution, to a wide range of formats, including JPEG, TIFF, BMP and PNG. Crystal engineering Take advantage of CrystalMaker’s flexible “molecule mode” to design new structures. Both Mac and PC versions let you record QuickTime movies as you work, with full control over frame rates and compression settings. There is also fully-automatic generation of QuickTime VR objects (ideal for multimedia presentations). Product Overview CrystalMaker 5 Fully-Interactive CrystalMaker includes real-time manipulation, molecular isolation tools and the ability to edit and design new structures: move, detach, duplicate, hide, delete groups of atoms; hide or repair molecular fragments; display lattice planes in any orientation; slice the crystal to investigate surfaces or internal planes. CrystalMaker lets you combine two or more structures in the same window, e.g., placing a molecule on a crystal surface, or investigating grain boundaries in an alloy. Visualize massive structures With virtually unlimited atoms, bonds and polyhedra, you can at last visualize results from latest-generation computer simulations. New features include molecule-tocrystal conversion and supercell generation: ideal for subsequent diffraction or modelling studies. Operating System Integration CrystalMaker is a cross-platform application, designed without compromise for the best performance and user experience on your choice of system: Mac or Windows. Whilst rival software has come and gone, we’ve been at the forefront of Mac scientific software for 14 years. Our Windows version, first launched in 2005, builds on our experience of user-centric software design, backed by solid scientific expertise—and leveraging the very-latest XP and Vista system technologies. Diffraction Support CrystalMaker is designed to work with our diffraction software: visualize a crystal structure in one window, then with a single menu command, simulate its diffraction properties. Optimized molecular crystals The Optimize Range commands make it easy to get just the right view of intact molecules in a molecular crystal. CrystalDiffract provides powerful x-ray or neutron powder pattern simulation, with the option of multipattern viewing, mixture simulation and direct comparison with observed data. Real-time parameter control gives you unprecedented power and flexibility: ideal for research and teaching applications. SingleCrystal provides display of reciprocal lattice sections, simulation of transmission electron diffraction patterns, and advanced stereographic projections. Featuring real-time tilt control, screen tools and extensive data and graphics export options, SingleCrystal brings diffraction firmly into the 21st century! Resources CrystalMaker includes a library with over 600 structures: edited, annotated and ready for immediate display. Additional resources include movies, VR objects, online help and user’s guide (with tutorial) , plus a vast array of online resources. Explore diffraction space With SingleCrystal you can display stereographic projections, reciprocal lattice sections and simulate electron diffraction patterns. Last, but not least, we are proud of our reputation for the very best technical support: free for the duration of your licence, and backed up by regular, free incremental program updates. In summary, CrystalMaker is your first-class ticket to the crystalline world. Product Overview CrystalMaker 6 What’s New in CrystalMaker CrystalMaker 8 for Mac (and the co-released CrystalMaker 2 for Windows) represents our biggest upgrade yet, with over 100 new features. The new program offers major new functionality, faster performance, and greatly-improved workflow. Seamless Workflow CrystalMaker’s interface has been streamlined to enhance workflow and provide seamless multi-structure browsing/animation. • Window toolbar. An optional toolbar provides shortcuts for important commands. Three default layouts are available, and can be extensively customized. • Extended Overview. The Overview Window provides drag-and-drop access to window views (which can be reordered, renamed, and updated), file favourites and undo states. Other options include full-screen “kiosk mode” and movie output. • Synchronize windows and views. Multiple structures, displayed in separate windows or View thumbnails, can now be synchronized to match the frontmost structure. A new dialog lets you choose which specific settings to synchronize. • Multi-structure animation. Effortlessly browse through structure sequences imported from CIF or PDB files; compare adjacent “frames” with a press of the arrow key, and save an animation with a single menu command. This is a great way to analyse structural changes and phase transitions! • Full-screen working. In Full Screen mode your structure is automatically zoomed to fill the screen, hiding unnecessary controls. Automatic menu bar and dock hiding is enabled, and you can summon up the appropriate palette windows to access the full range of tools, as needed. • Faster, more powerful text handling. Text file import is dramatically faster. Multistructure files are now loaded in the same window, with View thumbnails. PDB support now extends to crystals, with full connectivity data export. • New file formats supported. Four new file formats have been added, bringing the total to 15. The new formats are: ATOMS, GSAS (“.exp” files), MDL-Molfile and SDfile. • Access to online crystal structures. A new menu command takes you directly to the CrystalMaker Crystal Search web page, allowing you access to some of the world’s most comprehensive (and free!) crystal structures databases. Outstanding Display We’ve worked with our users to deliver new and improved display features including editable thermal ellipsoids, greater customization for atoms, intelligent auto labelling and much more. • Edit thermal ellipsoids. Isotropic and/or anisotropic displacement parameters can now be edited using a completely-revised Edit Crystal window. • Thermal ellipsoid sphere override. Thermal ellipsoid display can now be disabled for specific sites (usually hydrogen atoms), with small spheres (of user-defined size) displayed instead. • New spacegroups supported. Unconventional monoclinic and orthorhombic spacegroups are now recognized, and supported, by the Edit Crystal window. • Automatic label placement. CrystalMaker now gives you the option of manual or automatic label placement. In automatic mode, labels are positioned so as to minimize the chance of overlap with bonds—and you can opt to have the label text scaled as the structure is zoomed. Product Overview CrystalMaker 7 • Labels-to-textboxes conversion. Selected atom labels can be converted into static textboxes, which can then be edited and moved freely—ideal for final output. • Customize ball-and-stick sizes. We have opened up the program to allow user-defined relative- and minimum sphere radii for use in ball-and-stick and polyhedral plots. Interactive Control CrystalMaker makes it even easier for you to interact with your structure, including automatic plot scaling, fast view selection and easier range settings. • Fast view selection. The Set View Direction window now provides quick-view buttons for commonly-used view directions. • Live diffraction pattern rotation. Rotate a crystal structure in CrystalMaker and observe its diffraction pattern rotate in SingleCrystal—and vice versa. • Intelligent auto scaling. A new display mode adapts to changing plot size by automatically scaling the structure, letting you switch in and out of full-screen or kiosk modes, and providing smooth replotting as the window is resized. • Easier range settings. The Plot Range window has new buttons to display a single unit cell’s contents and to add integral numbers of unit cells along specific axes. • Supercells. Multiple unit cells can be merged into a single unit cell, thanks to the new Supercell command. This is especially useful when attempting to generate input for computer simulation studies. • Convert molecules to crystals. Convert aperiodic molecular data into periodic, crystallographic data. Ideal for working with computer simulations where tiling is required, or for simulating diffraction patterns from molecular data. • Discard Symmetry command. This command is useful when preparing input for computer simulation work, transforming your crystal’s spacegroup symmetry to P 1 whilst retaining the existing cell contents. • New Selection Commands. New commands to select textboxes, vectors or all objects have been added to the Selection menu. • List atom types command. The chemical composition of the currently-displayed model can be printed, broken down into numbers of atoms of each element type. Operating System Integration CrystalMaker 8 for Mac is designed to run natively on the latest versions of Mac OS X, 10.4 “Tiger” ,10.5 “Leopard” and 10.6 “Snow Leopard”. This universal binary application delivers optimum performance on both PowerPC & Intel processors. • Spotlight. CrystalMaker 8 includes full support for Spotlight, the advanced Mac search utility, letting you find your files by chemical composition, spacegroup, crystal system, cell parameters, density, and other crystallographic criteria. • Cover Flow & Quick Look. Instantly view the contents of your CrystalMaker binary files. Browse high-resolution previews in the Finder’s Cover Flow mode, and use thumbnail icons in other Finder modes. • Spell Checking (Mac). The notes pane of the Graphics window now gives the option of automatic spell checking as you type. • Fonts Panel. The Notes pane of the Graphics window now supports the Mac OS X Font Panel. This replaces the Text menu used in earlier versions of the program. • Handy User’s Guide. The full edition of the CrystalMaker’s User’s Guide is now available directly from the Help menu, for easy access as you work. Product Overview CrystalMaker A Seamless Workflow CrystalMaker is designed to provide the most-effective workflow for a wide range of crystallographic needs. This includes data import, structure building, bonding, manipulation, as well as graphics and video export. Key features include: • Auto-detection of major file formats • Support for multi-structure CIF, PDB, SDfile & XYZ files • Flexible interface for single and multi-structure working • Animated Views with movie output • Wide-ranging data export options • Video recording • Automatic generation of QuickTime Virtual Reality (QTVR) objects • Outstanding, high-resolution graphics export 8 Product Overview CrystalMaker 9 Automatic Detection of File Formats Unlike most other programs, CrystalMaker can auto-detect file formats: you don’t have to tell the program what format your file is in, or use tortuous import procedures; just drag-and-drop the file into the program, or use the program’s open command, and get to work right away. CrystalMaker can auto-detect and load the following file formats: • ATOMS • CCL • Chem3D Cartesian • CIF • CMTX (CrystalMaker text format) • CSSR • FDAT (Cambridge Structures Database) • GSAS • ICSD (Inorganic Crystal Structures Database) • MacMolecule 1 • Molfile • PDB (Protein Data Bank) • SDfile • SHELX • Struplo • XYZ Drag-and-drop for quick viewing CrystalMaker’s automatic format detection means you can quickly get to work with a wide range of text files. When loading text files, bonds and polyhedra can be automatically generated—but you always have the option of customizing this later, via the Edit Bonding and Model Options windows. Support for multi-structure text files Multi-structure text files (e.g., CIF, PDB, SDfile, XYZ) are processed in a veryconvenient and efficient way: each “sub-structure” is loaded, in the same window, as a separate View. All views are displayed, as thumbnails, in the Views palette, allowing you to seamlessly browse through multiple datasets, rearrange their order, create animations, slideshows, and output the results as a QuickTime movie. Managing Your Views Switch between multiple structures in full-screen mode, or tidy your multi-window layouts. Custom views can be created and synchronized. Flexible interface for single and multi-structure working CrystalMaker gives you the flexibility to work with multiple structures, in different windows—or browse a range of structures in the same window, via thumbnails in the Files pane of the Overview window. Powerful Synchronize commands make working with multiple structures—or different views of the structure—a breeze. Just set your preferred display options in one window, then choose the Synchronize command, to apply your settings to the other windows or views. You can even place one structure inside another, via the Place Molecule command: ideal for visualizing molecules on crystal surfaces, modelling interfaces, or depicting species within zeolite pores. Product Overview CrystalMaker 10 Animated Views with movie output CrystalMaker is unique in providing multiple, graphical undo levels, plus custom Views—for each structure. Views are convenient “bookmarks” for particular stages of your work; just click the Snapshot button to create a new View—it will be displayed, with a thumbnail icon, in the Views pane of the Overview window. The Views pane lets you organize your thumbnails (just drag-and-drop), rename them, and update any View to match the current display. Just click on a thumbnail to display it as an interactive model, or use the arrow keys to browse adjacent views. The Views pane is ideal for assembling the frames of a movie or animation. Use the new Play command to display an animation full screen, in “Kiosk” mode. The new Save as Movie command lets you output your chosen view sequence as a movie: ideal for use on the web, in presentations, or simply to emphasize structural behaviour, as shown below. Wide-ranging data export options CrystalMaker has a wide range of data export options, letting you easily share files in text format, generate input for other programs, or simply list coordinates and bond distances for a particular structure. Export file formats include: • Bond data (structural listing with distances and angles) • Coordinates • Coordination groups • Chem3D cartesian • CIF • CMTX (CrystalMaker text format) • HTML (web page summary, with picture) • MacMolecule 1 • PDB • XYZ CrystalMaker’s own text format is easy to read and includes detailed options for customizing the final plot. This is ideal if you need to computer-generate a sequence of structures with defined display settings. Product Overview CrystalMaker 11 Video recording CrystalMaker has advanced support for digital video recording, giving you complete control over frame rates, video compression, output size and quality. Control the video Use the handy Video Recorder palette to make movies whenever you want. The Video Recorder palette lets you customize your movie settings and control the subsequent recording. As you work, your manipulations are recorded as separate frames and you can pause the recording at any time. Another great way of recording movies is to assemble your frames, ahead of time, in the Views pane. That way you can sort through the frames you want to keep, rearrange them, and then save the entire collection as a QuickTime movie, using the new Save as Movie command. Automatic generation of QTVR objects QuickTime VR is a great way of providing self-contained fully-rotatable threedimensional models. These can be embedded within web pages, presentations, or multimedia packages—any software, in fact, that supports embedded QuickTime movies. Industry standard CrystalMaker supports the industry standard for digital video, QuickTime. The great advantage of QTVR is that it lets educators and multimedia authors focus on their content delivery, without getting side-tracked by complicated program interfaces, browser plug-ins, or other unnecessary details. CrystalMaker is the only program of its kind to produce fully-customizable QuickTime Virtual Reality (QTVR) objects for crystals and molecules. Simply choose the initial orientation for your crystal or molecule, toggle the Video Recorder into “VR mode”, then click the Record button to begin. You can customize the extent of 3D rotation (as well as the usual video output settings), then let the program automatically generate your VR movie. Product Overview CrystalMaker 12 Outstanding, high-resolution graphics export CrystalMaker uses its own graphics engine that is optimized to provide both outstanding on-screen display and ultra-high-resolution graphics export: a combination sadly lacking in a number of other programs which rely on video cards designed for computer games at screen resolution. With CrystalMaker, you can choose your output size, resolution, and format. For example, perhaps you’d like to output an A3 (17” x 11.5”) TIFF image at 600 dpi. Or maybe you’d prefer JPEG, PNG, Photoshop, PICT (Mac) or other formats? Simply choose your output format using the popup format menu in the File dialog. Pixel perfect Export high-quality photo-rendered graphics at your chosen output size and resolution. You have the option of including background art, with your structure superimposed. Windows users can opt to use transparent backgrounds (these work best in PNG format). Mac users can export certain types of models using Vector-based PICT graphics, although for best results with third-party programs we recommend using our high-resolution pixel-based graphics. Product Overview CrystalMaker Outstanding Display CrystalMaker gives you the flexibility to build all kinds of crystal and molecular structures, with extensive control over the range of atoms shown, bonding, colouring, display styles and graphics rendering. Key features include: • Easy structure building • Built-in model types • Customizable model options • Element colours and radius tables • Bond and polyhedra generation • Molecular crystal tools • Customizable rendering options • Depth profiling for massive/dense structures • Real 3D viewing in colour 13 Product Overview CrystalMaker 14 Easy structure building CrystalMaker enables you to build even the most complex crystal or molecular structures, quickly and easily, with only the minimum of data required to build massive structures. User-friendly data editors feature built-in spacegroup and symmetry handling: you can browse conventional and unconventional spacegroups, using the Spacegroup Browser, customize symmetry settings, then enter the minimum crystallographic information. CrystalMaker does the rest, building your crystal structure, applying your colour/radius presets, and displaying as much of the structure as you wish. Browse Spacegroups All conventional (and many unconventional) spacegroups can be chosen from the Spacegroup Browser. Built-in model types Unlike other programs, CrystalMaker lets you build and save each structure with more than one model type. Ball-and-stick, space-filling, wire-frame, stick, polyhedral, and thermal ellipsoid model types are immediately available and you can switch between them with a quick menu command. Each model can be extensively customized, and its settings saved with the structure in a CrystalMaker binary file. Customizable model options CrystalMaker provides extensive control over all aspects of your model’s display and rendering. You can edit settings on the basis of a selection (e.g., atom sphere colours and styles), or globally, by chemical element and/or crystallographic site. The Model Options window lets you control the default settings for your structure, such as atom sphere, ellipsoid and polyhedral styles, bond styles and colours, surface and unit cell options, etc. You can also set these as your defaults for new structures, via the window’s Save button. Polyhedra plus Polyhedral models provide extensive customization, with combinations of other model elements. Element colours and radius tables CrystalMaker comes with at least 8 pre-set tables of element colours and radii, covering all common structure/bonding types, including ionic and covalent structures. You can choose whichever table best fits your needs, or customize an element set, via the Element Editor. Colour coordinated Use the Site Browser to set atom colours, radii, visibility and labelling, on a site or element basis. You can easily tweak a particular structure’s colours and atomic radii using the Site Browser. Alternatively, just select one or more atoms in your model and use the Selection menu to change their attributes. Product Overview CrystalMaker 15 Bond and polyhedra generation Bonds can be generated automatically, using atom radius criteria, but you can fine tune, or override this using the Edit Bonding window (which also lets you preview coordination environments). Detailed information about interatomic distances is provided by the List Bonds command, which prints detailed tables or histograms in the program’s Log. Bond previews Use the Edit Bonding window to define bonding criteria, with instant coordination previews. Polyhedra—of any size or convex shape—are automatically generated during the bond search. Polyhedra are automatically shown for sites with the highest coordination numbers, and this can be edited using the Model Options window. Molecular crystal tools Working with molecular crystals can be tedious, particularly if one wishes to isolate a single molecule from a complex structure, and that molecule happens to straddle the unit cell boundary… Fortunately, CrystalMaker’s Optimize Range commands come to the rescue. You can display the optimum unit cell view, with fully-intact molecules, instantly. You can also opt to repair or hide molecular fragments—and of course the Selection tools let you hide any extraneous atoms without them being deleted. Custom polyhedra Generate polyhedra automatically, or build your own using the Make Polyhedron command. Customizable rendering options Rendering options can be applied to spheres, bonds, polyhedra and surfaces, using an advanced “Phong” illumination model. Whereas other programs rely on crude polygons to approximate spheres, CrystalMaker renders them pixel perfect, with spectacular photo-realistic shading. Translucent atoms CrystalMaker lets you display translucent atoms and surface overlays. Product Overview CrystalMaker 16 Depth profiling for massive/dense structures CrystalMaker provides a unique solution to the problems of visualizing massive or dense structures. With our Depth Profiling feature, distant atoms are faded out, and foreground atoms made translucent, thereby letting you see right inside your structure to a specified depth. A special depth control lets you choose, or edit, a depth profile function, which you can then apply to the current structure. With the Live Update option enabled, you can click-and-drag a slider control to tunnel through your material in real time. This is ideal for: • Seeing inside dense materials • Rapidly scanning a block of simulated structure • Understanding how surface structures vary with depth Real 3D viewing in colour CrystalMaker provides real-time 3D viewing, with a choice of stereo-pair or “redblue” modes. In “red-blue” you can choose between the traditional greyscale display or a new colour mode, for breathtaking “out-of-the-screen” visualization. 3D that really works CrystalMaker provides spectacular “out-of-the-screen” 3D viewing—in colour! Unlike other software, CrystalMaker’s colour 3D viewing runs in real time without expensive, proprietary video cards or clunky electronic viewing glasses. Just slip on a pair of lightweight (and very inexpensive) red/blue spectacles (easily fits over prescription spectacles) for an instant and truly spectacular experience. Even better, the 3D images can be projected using a standard video projector, so your colleagues and students can enjoy the experience too! Product Overview CrystalMaker 17 Fully-Interactive CrystalMaker is unique in providing a fully-interactive and immersive environment, designed to let you manipulate your structures in the most intuitive manner. The floating Tools palette gives easy access to screen tools in both standard and fullscreen modes, allowing you to customize selected regions of your structure, place molecules, create surfaces and engineer new materials. Key features include: • Extensive range of screen tools • Instantly hide/show groups of atoms • Molecule–Crystal conversion • Place different structures into same model • Easy surface/slab creation • Supercell generation Product Overview CrystalMaker 18 Extensive range of screen tools CrystalMaker’s floating Tools palette provides a wide range of tools for manipulating, measuring and editing a structure. The Rotate tool lets you rotate and zoom a structure in real time; other commands are available to selectively scale or move (translate) the model. Selection tools provide single-click (Arrow), drag-select (rectangle), and region selection (polygon and lasso tools). Atom info Use the Atom Info tool to identify clicked atoms, with the option of bond data printed in the program Log. Measurement tools include: • Atom info • Distance (3D and 2D options) • Angle (3D and 2D) • Torsion Angle • Lattice plane Instantly hide/show groups of atoms You can easily tweak your display by selectively hiding atoms on the basis of their position (selection tools), chemical element or site type. The Zapper and selection tools let you hide specific atoms, perhaps to hide under-bonded atoms at the edge of a model, or to emphasize a specific structural group, as illustrated below. You can also use the Site Browser’s Visibility checkboxes to toggle all atoms of a particular element (e.g., oxygen) on or off, or to show or hide specific sites. This is helpful when working with complex structures, as it allows you to “see the wood for the trees”. Molecule–Crystal conversion CrystalMaker works in one of two possible modes for any particular structure. The usual, “crystal” mode, relates the current display to an underlying crystallographic basis, with spacegroup symmetry and lattice translations. In “molecule” mode, the crystallographic information is discarded, and one instead deals with an isolated group of atoms in space. Sometimes it is useful to be able to break the crystal symmetry, especially when dealing with defect structures, or when you wish to combine multiple structures in the same display. You can use the Crystal-to-Molecule command to accomplish this. Crystal engineering Take advantage of “molecule mode” to design new structures. The reverse is also now possible: converting an isolated block of material (e.g., the output from a computer modelling calculation) into a regularly-tiled lattice, via the Molecule-to-Crystal command. This has the useful side effect of allowing you to simulate diffraction properties for the new crystalline material. Product Overview CrystalMaker 19 Place different structures into same model In “molecule” mode, you can combine different structures into the same model, via the Place Molecule command. This is an excellent way of visualizing domain boundaries in alloys and placing molecules on crystal surfaces or inside zeolite channels. You can repeat this process as many times as you like, building up complex assemblages of materials. Individually-placed “molecules” can, if they are self-bonded, be independently manipulated, via the Selection tools and the Rotate Selection mode. Boundary control Use the Place Molecule command to create oriented intergrowths or domain boundaries. Easy surface/slab creation CrystalMaker lets you create oriented surfaces or slabs in a number of easy ways. You can use Selection tools, in conjunction with the View Direction command, to carve out a chunk of material; you can use the Depth Profiling feature to visualize a surface at depth in a material; or you can use the most elegant method of all: the Lattice Plane command. The Lattice Plane command displays an oriented, translucent plane, slicing through the centre of your crystal, in your specified orientation. The plane can be moved, along its normal, by dragging it with the Lattice Plane tool. To create a surface, simply drag the lattice plane to an appropriate position, then use the Slice Model command to hide atoms on one or other side of the plane. This can be repeated to create a slab, or used with other orientations to create crystal morphologies. Crystal faces The Lattice Plane tool can be used to reveal the strutural constraints behind crystal morphology. Supercell generation The new Define Supercell command lets you convert multiples of an existing unit cell into a much larger, “Supercell”. You can define the size of the supercell (numbers of cells along the crystallographic axes), and CrystalMaker handles the symmetry transformation for you. Superlattice properties This 2x2x2 spinel supercell was created to model “superlattice reflexions” in diffraction patterns, caused by cation ordering. Supercell generation is a great preparation for simulating diffraction properties from defect materials. You can use CrystalDiffract and SingleCrystal to simulate the resulting “superlattice” reflexions. Product Overview CrystalMaker 20 Operating System Integration CrystalMaker is a cross-platform application, designed without compromise for the very-best performance and user experience on your choice of operating system: Mac or Windows. Key features of the Mac version include: • Latest “Snow Leopard” interface design • Universal binary • Spotlight plug-in • Cover Flow and Quick Look plug-ins • Rich-text editing and spelling support Key features of the Windows version include: • Designed for Windows XP, Vista & Windows 7 • Unified product installer • Windows Explorer file previews and info tips • Rich HTML-based online help system • Inter-application communication • Windows active directory support Product Overview CrystalMaker 21 Mac System Integration Whilst rival software has come and gone, we’ve been steadfast in our support for the Mac, dating back to 1994. CrystalMaker was the first application of its type to support PowerPC, the first to run natively on Mac OS X, the first to run natively on Intel, and now the first to leverage key “Leopard” and “Tiger” technologies such as Cover Flow, Quick Look and Spotlight. Universal performance CrystalMaker runs natively on both PowerPC and Intel Macs. Latest “Snow Leopard” Interface Design CrystalMaker 8.2 for Mac is designed to run natively on the latest versions of Mac OS X, 10.4 “Tiger” ,10.5 “Leopard” and 10.6 “Snow Leopard”. Windows, sheets and data browsers have been updated to take advantage of new operating system capabilities. This application is provided as a universal binary, delivering native performance on both PowerPC and Intel processors. Universal Binary CrystalMaker for Mac is shipped as a Universal Binary application: this runs natively on both Intel- and PowerPC hardware, ensuring that you get the very-best performance, regardless of which Mac you own. In our own tests, an Intel-native version of CrystalMaker was approximately 250% faster, when measured on an Intel Mac, compared with a non-native application. Spotlight CrystalMaker 8 includes full support for Spotlight, the advanced Mac OS X search utility. As part of this support, the program provides a plug-in that works with the operating system and Spotlight, indexing the contents of your CrystalMaker binary files in the background. Once Spotlight has finished indexing your structures, you can search and find files using a wide range of structural criteria, including: • chemical composition • spacegroup • crystal system • unit cell parameters (a, b, c, a, b, g) • unit cell volume • density • presence of thermal (displacement) parameters • any information saved in your notes Spotlight integration Detailed information about a crystal is available right from the Finder— thanks to our Spotlight plug-in. With Spotlight you have the option of multiple search requests such as “all files containing the elements Ca and O with cubic symmetry, and a density greater than 2500 kg/m3”, as shown in the illustration below: Product Overview CrystalMaker 22 Cover Flow and Quick Look Instantly preview the contents of your CrystalMaker binary files. Browse through high-resolution previews of your CrystalMaker binary files in the Finder’s Cover Flow mode. View preview icons in other Finder modes. (You will need to ensure that any old files are re-saved in CrystalMaker 8 to enable this feature.) Rich Text Editing and Spelling Support CrystalMaker’s text windows, including the program Log and Notes pane, support rich-text editing with drag-and-drop support. The Notes pane allows you to have your spelling checked as you type, and supports the Mac OS X Font Palette. Product Overview CrystalMaker 23 Windows System Integration The Windows version of CrystalMaker was launched in 2005, and uses the latest technologies on Windows XP and Vista, uncluttered by the compromises of legacy systems. Designed for Windows XP, Vista & Windows 7 CrystalMaker for Windows was built, for scratch, to support Windows XP and later operating systems, including Windows Vista. The program uses the latest system technologies, and does not require legacy (and slow) interfaces. Unified product installer CrystalMaker for Windows uses a unified “umbrella” installer, allowing you to customize the installation process for all our software applications—including CrystalDiffract, SingleCrystal, as well as CrystalMaker. Supporting resources, including examples files, multimedia extras, documentation and online help, can be optionally installed. Windows Explorer file previews and info tips A new plug-in allows display of file previews on both XP and Vista operating systems, together with info tips, giving file/content information. Rich HTML-based online help system CrystalMaker uses a cross-platform, forward-looking HTML-based online help system, that provides rich text, graphics and hyperlink control. Inter-application communication Our program architecture allows inter-application messaging, letting you send structural data from CrystalMaker to CrystalDiffract or SingleCrystal. You can visualize a crystal structure in one window, then simulate its diffraction properties in other windows. Windows active directory support Active directory support gives you more flexibility when you purchase a multi-user, Classroom or Site licence. Multiple users can log-in from different locations on a network and still access their personal settings and files. Product Overview CrystalMaker 24 Diffraction Support CrystalMaker is designed to work with our two diffraction programs to provide a complete crystallographic toolkit, covering x-ray and neutron powder diffraction, reciprocal space, transmission electron microscopy, stereographic projections and of course visualization of the structure itself. Key features of CrystalDiffract include: • Works with CrystalMaker • Powder diffraction simulation • Interactive parameter control • Multi-pattern display with mixture control • Comparison with observed data • Comprehensive data output options Key features of SingleCrystal include: • Works with CrystalMaker • X-ray & Neutron diffraction simulations (including Laue & Precession) • TEM diffraction pattern simulation • Real-time rotation, scaling and measurement • Overlay of diffraction data/observed pattern • Measurement & auto-indexing tools for observed data • Stereographic projections with symmetry support Product Overview CrystalMaker 25 CrystalDiffract Features CrystalDiffract is our solution for x-ray and neutron powder diffraction. It is designed both as a teaching and a research tool: students can learn about powder diffraction, and how this is affected by experimental and sample effects. Researchers can quickly simulate patterns, for easy comparison with observed data. Quick and Easy Just drag-and-drop any CrystalMaker crystal binary file into CrystalDiffract to view its simulated powder pattern. The program is ideal for characterising synthesis experiments, working with mixtures, or understanding particle size/strain effects. Whatever your background, CrystalDiffract provides a sound basis for working with powder diffraction. Works with CrystalMaker If you have CrystalDiffract installed on your system, then you can simulate x-ray or neutron powder diffraction patterns, directly from CrystalMaker. Simply choose the Powder option from CrystalMaker’s Diffraction Pattern submenu. CrystalDiffract will be automatically launched (if it isn’t already open), and your crystallographic data—including site occupancies and atomic displacement parameters—transferred to CrystalDiffract for its diffraction calculation. Powder diffraction simulation CrystalDiffract lets you simulate x-ray or neutron powder diffraction patterns, with a choice of experimental types including: • Angle-dispersive (theta/two-theta) • Angle-dispersive (d-spacing) • Angle-dispersive (reciprocal d-spacing) • Energy-dispersive • Time-of-flight Dual wavelengths CrystalDiffract lets you specify the wavelength, with support for dualwavelength (Ka1/a2) radiation. You have extensive control over the simulation process, including peak profile types (Gaussian, Lorentzian, Pseudo-Voigt—with eta parameter control), peak width (instrumental broadening) wavelength(s), as well as sample size and strain parameters. High-quality graphics Simulated diffraction patterns can be displayed as greyscale films or graphs. Individual patterns can be selected and their plot parameters edited, e.g., line width, colour, style (dashed, dotted, continuous). Peaks can be automatically labelled (any combination of Miller indices, d-spacing, x-value or phase name) and you can specify an intensity threshold below which labelling is suppressed. Product Overview CrystalMaker 26 The full-feature version of CrystalDiffract lets you print diffraction patterns at high resolution. You also have the option of exporting diffraction data—including multiple profiles—as text files, for display in other programs. Interactive parameter control A key feature of CrystalDiffract is the power it gives you to adjust experimental and sample parameters to see how these affect the diffraction process. Parameter control CrystalDiffract lets you adjust many instrumental and sample parameters—including composition—real time. You can use the Parameters list to select specific parameters, such as particle size or a cell parameter, then click-and-drag a slider control and watch the diffraction pattern change in real time. This is ideal for learning about diffraction, but can also be instructive when comparing simulated data with real, observed data. Multi-pattern display with mixture control CrystalDiffract gives you the flexibility to compare multiple diffraction patterns in the same window. You can have the patterns automatically stacked in Film or Graph modes, or manipulate individual patterns, adjusting their relative scaling and x/y offsets. You can instantly toggle between separately-displayed patterns, and a single, simulated mixture. The Parameters list lets you adjust the relative proportions of mixture components: again, this happens in real time. Comparison with observed data Real diffraction data can be loaded as xy text files. You can drag-and-drop any number of these files into a diffraction window, for ready comparison with simulated patterns. Unlike other programs, CrystalDiffract even lets you combine multiple observed patterns into a single, “observed mixture”. Comprehensive data output options CrystalDiffract has powerful data output options. You can browse individual diffraction pattern data onscreen, sort by d-spacing, intensity or any other parameter, then save the result as a text file. Residual display Compare real and observed diffraction patterns in the same window, with the option of Residual display. The program’s Export submenu gives you additional options. You can export a detailed diffraction listing, including structural data plus peak intensities, indices, positions, etc. There is also the option to export full structure factor data: not something you might expect from a powder diffraction program! Product Overview CrystalMaker 27 SingleCrystal Features SingleCrystal is our solution for anyone who needs to visualize single-crystal diffraction patterns, the reciprocal lattice, or work with stereographic projections. Here is an elegant, easy-to-use program to bring a dusty area of crystallography firmly into the 21st century! Quick and Easy Just drag-and-drop any crystal binary file into SingleCrystal to view a simulated diffraction pattern in the saved orientation. Design Award SingleCrystal received an Apple Design Award in 2007. The judges praised SingleCrystal for making a specialized area of science accessible and fun! Works with CrystalMaker As with CrystalDiffract, SingleCrystal can be invoked directly from CrystalMaker’s Diffraction Pattern submenu. Your currently-displayed structure is used to simulate a diffraction pattern or reciprocal lattice section, in exactly the same orientation as your crystal model. Reciprocal lattice display and diffraction pattern simulation -7 0 0 -6 -2 0 -6 0 0 -5 -2 0 -6 2 0 -5 0 0 -4 -1 0 -4 0 0 -3 -1 0 -5 2 0 -4 1 0 -3 1 0 -2 -3 0 -2 -2 0 -2 -1 0 -2 0 0 -2 1 0 -2 2 0 -2 3 0 -1 -3 0 -1 -2 0 -1 -1 0 -1 0 0 -1 1 0 -1 2 0 -1 3 0 0 -2 0 You can opt to display a reciprocal lattice section, or a weighted reciprocal lattice section. The orientation of your crystal is set by specifying a view direction—or you can simply click-and-drag with the mouse to rotate your crystal, or use one of the rotation buttons in the toolbar. 020 1 -3 0 1 -2 0 1 -1 0 100 110 120 130 2 -3 0 2 -2 0 2 -1 0 200 210 220 230 3 -1 0 4 -1 0 310 400 410 5 -2 0 500 520 6 -2 0 600 620 700 Colourful phases SingleCrystal does what no experiment can ever do: show phase information, as well as intensities. SingleCrystal lets you simulate X-ray and neutron diffraction patterns, using a choice of experimental modes including Laue Cylinder, Front Plate, Back Plate; and Precession patterns. TEM diffraction patterns can also be simulated, with control over thickness, wavelength, beam convergence, intensity saturation, and much more. Real-time rotation, scaling and measurement A great feature of SingleCrystal is its real-time interactivity. You can rotate diffraction patterns with the mouse (rather easier than using real-life tilt controls!), scale the pattern, adjust intensity saturation (“beam current”), and measure distances, angles and peak parameters—all interactively. Live Diffraction Link You can now rotate your crystal structure in CrystalMaker, and observe its diffraction pattern rotating automatically, in SingleCrystal (or vice versa!). A great way of understanding your diffraction properties, and a brilliant teaching tool! Product Overview CrystalMaker 28 Overlay of diffraction data/observed pattern Tilt control Reorient your sample using the toolbar’s tilt controls. As with CrystalDiffract, you can compare real diffraction data with simulated data. Just drag-and-drop an image of your real pattern into SingleCrystal, and it will appear as a backdrop, with your simulated pattern overlain for easy comparison. This is particularly helpful when dealing with domain or twinning structures, as illustrated in the following example. Auto-Indexing If you need to index a real diffraction pattern, SingleCrystal is here to help! Use the new Grid tool to identify your observed reflexions, then have the program automatically index your pattern—and update the crystal’s orientation—with a single menu command. (You can also generate a “Zone Axes File” with tabulated view directions, reciprocal lattice ratios/angles, etc., for use in manually indexing a pattern.) Stereographic projections with symmetry support SingleCrystal brings the arcane world of stereographic projections firmly into the 21st century, with real-time interactive display, high-quality smoothed graphics, colour-coded poles and traces—and the option of displaying symmetry-related poles and traces. Explore symmetry Use the stereogram to display symmetry-related plane normals, vectors (zone axes) and their traces. SingleCrystal’s graphics—including the diffraction pattern and the stereographic projection—can be copied to the clipboard, printed, or exported, as high-resolution vector or pixel-based graphics. Product Overview CrystalMaker 29 Resources To learn more about CrystalMaker and how to get the most out of using the program, we have prepared the following resources. For more information visit the CrystalMaker web page at www.crystalmaker.com/crystalmaker. User’s Guide The definitive guide to CrystalMaker is provided in PDF format, and accessed when running the full version of CrystalMaker, using the Help menu. Tutorial Included within the full user’s guide is a handy tutorial, designed to get you up-andrunning as quickly as possible. Setup Guide The full version of CrystalMaker includes a colour-printed setup guide, covering installation and general use of the program. This is organized in terms of a typical workflow, from getting data into the program, to display, manipulation, and output. Quick Tour (Mac) Accessed via the program’s Help menu, the Quick Tour is an illustrated PDF document, highlighting the new features available in CrystalMaker 8 for Mac. New Features Browse the illustrated news articles about the program’s features. www.crystalmaker.com/crystalmaker/whatsnew.html Online Tutorials Visit the Support section of our website for a wide range of illustrated tutorials, program tips and user forums. www.crystalmaker.com/support CrystalMaker Gallery See examples of CrystalMaker in action, via our interactive web gallery (requires JavaScript). www.crystalmaker.com/crystalmaker/action Free Demo Free demonstration versions of CrystalMaker, CrystalDiffract and SingleCrystal are available from the CrystalMaker website. Each demo includes online help, a user’s guide and examples files. www.crystalmaker.com/downloads Product Overview CrystalMaker 30 Technical Specifications Data Import • ATOMS • CCL • Chem3D Cartesian • CIF (Crystallographic Interchange File) • CSSR (Daresbury Laboratory) • CMTX (CrystalMaker text format) • FDAT (Cambridge Structures Database) • GSAS • ICSD (Inorganic Crystal Structures Database) • MacMolecule 1 • Molfile • PDB (Protein Data Bank) • SDfile • SHELX • Struplo • XYZ Data Export • Chem3D Cartesian • CIF • MacMolecule 1 • PDB • CrystalMaker Text • CrystalMaker Elements • CrystalMaker Bonds • CrystalMaker Coordinates Listing • CrystalMaker Crystal Coordination • CrystalMaker Visible Coordination • HTML (web page generation) • XYZ Symmetry Handling • Auto-recognition of spacegroup symbols for all 230 conventional spacegroups, plus all alternate settings listed in the International Tables for Crystallography • Auto-recognition of Schoenflies symbols and/or spacegroup numbers • Symmetry Browser allows easy navigation and searching through crystal systems, lattice types and spacegroups, with optional display of unconventional settings and detailed spacegroup information. • Symmetry Options dialog allows editing of lattice types, general equivalent positions and origin offsets • Automatic definition of symmetry-constrained lattice parameters (Constrain lattice parameter option) Product Overview CrystalMaker 31 Atom Colours and Radii • Automatic recognition of element symbols, matching current global element table • Elements Dialog provides editing of global element specifications, plus import/ export of atom colour/radius values • Preset atom specifications provided for Shannon & Prewitt “crystal radii”, covalent tetrahedral & octahedral coordination; Cambridge Structures Database atomic radii; atomic radii Bonding and Polyhedral Options • Auto-Generate Bonds option • List Bonds command—provides bond searches and full, concise, or histogram output around specified sites • Bond Editor (Edit Bond Specs dialog) allows control over individual bond specifications, including minimum and maximum distances for bonding between pairs of chemical elements. • Multiple bond specifications for the same element pairs make it possible to distinguish covalent from hydrogen bonding (e.g., H–O versus H...O). • Automatic generation of polyhedra, following bond generation. Rendering Options • Phong rendering model, with full control over ambient, diffuse and specular reflection from atom spheres, bonds, polyhedra and surfaces • Polyhedral frame highlights • Ambient and Point light intensities • Depth Fading—control and extent • Depth Profiling with real-time zoom control (Mac) • Perspective view distance • Stereo separation • Red/blue stereo standout and angular separation Automatic Model Types • Ball-and-stick • Stick • Space filling • Wire frame • Polyhedral—including combinations of the other model types • Thermal Ellipsoids • Surface Overlay option—with choice of density fill, dot surface or translucent smooth shading Model Options • Extensive choice of photo-rendered or colour/black-and-white atom sphere and ellipsoid styles for individual sites • User-defined thermal ellipsoid probability value with option of plotting selected sites as spheres of an arbitrary size (e.g., H atoms). • Extensive choice of bond styles for particular bond specifications (e.g., “C–O”), or for individually- selected bonds. • User-defined relative bond radii for ball-and-stick and stick model types. • User-defined sphere radii, including control over ball-and-stick spheres. • Extensive choice of polyhedral styles for different sites or atoms (Molecule mode). • Scale line width option for atoms, bonds and polyhedra Product Overview CrystalMaker Display Options • Single, or multiple unit cells; user-defined line width, style and colour • Display of “xyz” or “abc” axial vectors • Display of atom labels, by element type, site, or for individually-selected atoms. Choice of global site labels, chemical element, atom numbers or z-coordinate display, with user-defined font and positional settings (with auto option). • Vectors can be added to any selected atom, in user-specfied orientations [UVW], colour and length • Lattice plane display (user-defined orientation, colour and translucency) • Background pictures • Background colours and/or gradient fills • Text boxes, with lines or arrows. Custom-defined colours, fonts. Molecular Crystal Tools • Hide “stranded” (under bonded) atoms option • Hide Molecular Fragments option • Repair Molecular Fragments option • Display of optimum unit cell (complete unit cell contents with fully-intact molecules) • Select Entire Molecule option • Hide Other Molecules option Measurement • Nearest-neighbour bond searches: user-specified search distance from specified sites. Choice of detailed, concise, or histogram display. • Bonds listing, with coordinates, distances and angles for every site. • Screen ruler and real-time distance tool • Info tool lists coordinates and bonding details for clicked atom • Distance between selected atoms • Included angle between 3 selected atoms • Torsion angle between 4 selected atoms • Distance from selected atom(s) to a displayed lattice plane • Centre-of-gravity of selected atoms, with distances to centre • Angles between specified lattice vectors and/or lattice plane normals • Best-fit lattice plane through selected atoms • Unit cell volume (printed in Bonds output file) • Calculated density (Bonds file) • D-spacings (displayed in Show Lattice Plane dialog) Manipulation • Mouse-driven structure rotation • Mouse wheel support for x, y and z rotation (via keyboard modifiers) • Accelerated rotation option • Toolbar rotator pad for rotation through precise angle steps • Auto Rotate command • Toolbar scale buttons, with accelerated scale option • User-defined scale • Mouse-driven movement of entire structure (Move tool) • Mouse-driven movement of individually-selected atoms (Arrow tool) • View down any lattice vector or plane normal • Display all atoms within a preset range of fractional coordinates (not limited to integral numbers of unit cells!) • Hide atoms by site, element, or individual selection • Selection of entire molecule containing one selected atom • Iterative selection of nearest neighbours • Crystal—Molecule conversions (two-way) • Place Molecule option 32 Product Overview CrystalMaker 33 Graphics Output • Vector PICT, with user-specified size and resolution (Mac version). • Photo-realistic pixel-rendered TIFF, JPEG, BMP, PNG, etc., with user-specified size and resolution. • Transparent background option (Windows version) • PDF file (via the Print command, Mac version) • High-resolution printing • QuickTime (linear) movies. User-defined movie settings. • Automatic generation of QuickTime Virtual Reality (VR) object movies. CrystalMaker can also import a wide range of graphics files, for use as background pictures. Window Options • Different structures plotted in different windows. • Display different views of the same structure in different windows • Display different structures in the same window, via the Files pane • Bookmark your favourite views, using the Views pane of the Overview window • Tile, Stack and Synchronize Windows commands Assistance • Colour-printed setup guide • 175-page user’s guide (PDF format), available from Help menu. Includes tutorial • Online help (HTML based) • Context-sensitive help links • Contextual popup menus • Tool tips • Automatic update checking • Web-based user forums • Free technical support to the licensed user(s), for the duration of the licence Program Limits • Virtually unlimited (2 billion) atoms, bonds, polyhedra • Unlimited file favourites and window views • Multiple (100) undo levels per window What’s in the Box • Colour-printed setup guide • Red/Blue stereo 3D glasses • Mac or Windiows CD-ROM • Crystal structures library (600+ annotated structures) • Examples files illustrating program features • QuickTime movies, VR objects and background pictures • Program with integrated online help (Mac or Windows) • Fully-comprehensive user’s guide, in searchable PDF format, includes tutorial • Quick Tour guide (Mac)—available from the program’s help menu CrystalMaker is shipped in a deluxe DVD-style presentation case, with featurepacked CD-ROM (installer program provided for Windows version), printed setup guide and 3D spectacles. Product Overview CrystalMaker 34 Product Overview CrystalMaker 35 1994 – 2009 15 Ye ars of CrystalMaker CrystalMaker® S O F T W A R E CrystalMaker Software Limited Centre for Innovation & Enterprise Oxford University Begbroke Science Park Sandy Lane, Yarnton, Oxfordshire, OX5 1PF, UK Tel: +44 1865–854804 • Fax: +44 1865–854805 sales@crystalmaker.com • http://www.crystalmaker.com