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CrystalMaker® 2.0 for Windows Multi-Structure Visualization Comes of Age Overview Features |
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8 January 2008. CrystalMaker Software Ltd is delighted to
announce the immediate availability of CrystalMaker 2.0 for
Windows XP and Vista. This is our biggest upgrade yet, with over
100 new features, including a new interface, multi-structure
animation, depth profiling, supercells, and much more...
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Streamlined Interface CrystalMaker 2.0 features a streamlined user interface, designed to boost productivity. The default window count has been reduced from five, down to three windows, thanks to a new Sidebar in the Graphics window (which can show both a Site Browser and a Notes pane) and an enhanced Overview window. Overview Power The Overview Window has been completely redesigned, with a new Log pane (replacing the old Output window). Custom window views, favourite files and undo states are represented by thumbnails in three other panes. Thumbnails can be resized using a slider control, rearranged (Views and Files) and renamed (Views). You can use the Files pane to keep track of your favourite files: just drag-and-drop any file or folder into the pane; any text or CrystalMaker binary files will be loaded and thumbnails shown. You can display animated slideshows using the contents of the Files pane or the Views pane. You have the option of a full-screen "kiosk" mode in which all interface elements are hidden: great for presentations! |
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Depth Profiling CrystalMaker allows you to accentuate the three-dimensionality of your structures by fading out more distant atoms (depth fading). A new feature is the ability to control the opacity of foreground atoms. You can make these atoms transparent, with more distant atoms gradually becoming visible - whilst the most distant atoms fade into the background again. In this way, you can look "inside" a dense, complicated structure - with the option of profiling different depths in the material. |
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Profiling the faujasite structure. The new Depth Zoom tool
can image thin slices through the bulk of an extended crystal lattice.
These images - taken just a few Angstroms apart - show cage clusters
(left) and a ring structure (right).
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Applications of depth profiling might include:
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Multi-Structure Animation Effortlessly browse through huge numbers of structures saved in multi-structure 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! Synchronize Views. Use the new Synchronize command to synchronize all of your Window's views. This way you can set your model type, bonding, colours and plot range for one structure, and have your changes automatically applied to all other structures. Instant Movie Generation. Rename and rearrange the subviews, then use the Overview Window's Actions menu to automatically save the views as an animation, in QuickTime movie format. |
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Analysing structural changes associated with a phase transition
in a silicate mineral. Here, a series of view "snapshots" can
be used to create an animation or movie.
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Model Options CrystalMaker 2.0 includes a huge number of improvements to model generation and display. Some of the key changes include: Label Overlap Correction. Atom labels can now be automatically positioned so as to minimize the chance of overlap. This is a new option (checkbox) in the Labels pane of the Model Options window (which also gives the option of static label positions). Label positioning is further enhanced by using font metrics to better vertically- adjust the label. |
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| CrystalMaker image of an organic molecule, with labels automatically positioned so as to avoid overlap. |
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Another new Atom Label option is to have labels automatically
rescaled as a structure is zoomed. This can be useful when you need
to start with an extended structure (e.g., a molecular crystal) and
then cut away much of the structure to reveal a sub unit. The atom
label size automatically adjusts as the scale changes, so that
labels remain correctly proportioned relative to atom spheres.
Labels-to-Textboxes Command. As an alternative to relying on automatic label positioning, you can opt to convert selected atom labels into textboxes. These can then be edited and moved freely - ideal for final output. Thermal Ellipsoid Override. One of our most frequent requests was the possibility of turning off thermal ellipsoid display for specific sites in a structure, and to plot those sites (generally H atoms) as small spheres. The Atoms pane of the Model Options window now includes thermal ellipsoid checkboxes in its scrolling list. Turning off a checkbox causes that site to be plotted as a sphere. The sphere radius can be customized using the new Thermal Ellipsoids Sphere Radius text edit field. Customize Ball-and-Stick Sizes. We have opened up the program to allow control over the relative radii of ball-and-stick spheres (compared to space-filling spheres), and the minimum radius used to plot ball-and-stick spheres. Thesesettings can be edited via new text fields in the Atoms pane of the Model Options window. File Import/Export CrystalMaker 2.0 for Windows now supports import of structural data from GSAS experiment (".exp") files, and the loading of PDB files as crystals (rather than as molecules). Text files now load much faster thanks to an improved status display. This is particularly evident for multi-structure PDB and CIF files. Those files are also loaded in a more convenient manner, with the individual structures displayed as separate Views in the same window: allowing easy browsing and animation. Supercells Multiple unit cells can be merged into a single unit cell, thanks to the new Transform > Supercell command. This is especially useful when attempting to generate input for computer simulation studies: you can generate a new, much larger unit cell, simply by specifying how many old cells to use along each of the x, y and z axes. |
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| A 2×2×2 supercell in the oxide mineral spinel, showing a dopant (green atom). This modified crystal structure can be used to simulate superlattice reflexions in powder or single-crystal diffraction patterns. |
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A related, Discard Symmetry
command lets you transform your existing spacegroup to P 1 symmetry;
the asymmetric unit is extended to include the full cell
contents).This may be useful when preparing input for computational
studies.
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Other Changes CrystalMaker 8 contains numerous new features and "under the hood" improvements.
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© 2009 CrystalMaker Software Limited. All rights reserved worldwide. |
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