Newsletter

Wednesday 6 July 2016

It's been eight months since our last newsletter and a lot has happened in that time: we've had a number of free CrystalMaker® updates, met many of you at conferences (San Diego and Phoenix), sponsored three societies and, last but not least, completely rewritten CrystalDiffract® for Windows...

CrystalDiffract® 6.6

CrystalDiffract icon Spacer

Our interactive powder diffraction software, CrystalDiffract 6, has just had a major update, bringing it to version 6.6. This comes on top of last year's "leapfrog" 6.5 release, which followed the earlier, 6.0 release. The latest update is all about "under the hood" changes: improving performance, compatibility and convenience.

CrystalDiffract 6.6 at a glance:

This major update is FREE to registered CrystalDiffract 6 users. Download your copy from our website today.

Out with the Old, in with the New

Windows 10 Logo

CrystalDiffract 6.6 for Windows is all new. Nothing remains of the old program, which was developed using Microsoft Foundation Classes. In its place comes a brand new .NET program, written in C#, and taking advantage of new system features and native functionality in the Windows operating system.

CrystalDiffract for Windows is now comparable in design and structure to the Mac version: both are written using native object-oriented technologies for their respective operating systems (C#/.NET for Windows; Objective-C/Cocoa for Mac).

This was a monumental task, and it underlines our commitment to quality: writing the best code with the best performance and design for each operating system. This "no-compromise" design certainly isn't the most "efficient" way to program, but it yields the best outcomes, and that's why we do it.

Compatibility

CrystalDiffract 6.6 for Windows requires Windows Vista (Service Pack 3) or later. For users still running Windows XP, we have provided a special 6.5.6 update which provides a number of bug fixes and other improvements.

Performance and Precision

Heavy-duty diffraction simulation can be challenging. This latest version uses 64-bit precision throughout, with new algorithms and better memory access to speed up intensity calculations. In our speed tests, Mac version 6.6 was more than twice as fast as version 6.5 when simulating diffraction from a massive protein crystal. The Windows version showed even more impressive gains compared to its predecessor.

Tip: CrystalDiffract Defaults

CrystalDiffract's Preferences panel lets you control the program's default settings - including the extent of any diffraction simulation. The Profile pane lets you specify a maximum number of reflexions and/or set a minimum d-spacing. For most structures this won't be necessary, but if you work with massive unit cells, you might want to dial back the number of reflexions used for typical simulations.

Fast Parameter Mode

Interactive control over sample and diffraction parameters is a CrystalDiffract hallmark. However, for massive structures such as proteins, real-time control may not be possible - until now. The new "Fast Parameter Mode" (an option in the Preferences panel) permits very-fast adjustments of wavelength, preferred orientation - and even unit cell dimensions - for massive structures. The program optimizes the number of reflexions to match the current display (or, in extreme cases, will prioritise low d-spacing reflexions). Once adjustments are complete and the program is idle, the remaining reflexions will be generated and the full pattern prepared for subsequent display when you scroll or zoom.

CrystalDiffract 6.6 resizable scroller thumb

Using the Ruler's cursors to define a zoom box.

Tip: Zoom to Cursors

Following popular demand, we have added the equivalent of a "Marquee" tool to CrystalDiffract 6: this lets you define a rectangular range which will be zoomed to fill the diffraction pane.

Rather than introduce a "modal" tool, we've kept CrystalDiffract's interface clean, and instead leveraged the horizontal and vertical cursors already built into the program, via its Ruler tool (which you can toggle on or off via the window toolbar).

Simply position the ruler's vertical (left and right) cursors to define your x-range; then adjust the horizontal cursor to define the maximum y-range. Finally, right-click on the ruler and choose Zoom to Cursors from the Ruler's contextual menu (as illustrated).

Refreshed Interface

CrystalDiffract's Patterns List (sidebar) has been streamlined, with more functionality in its contextual menu, and a new Add button in the window toolbar (the former "+" and "Actions" popup menu buttons in the window's bottom-left corner are now gone.) Improvements have also been made to the Reflexions List resizing and to the Scroller - allowing easy adjustment of the reflexion range.

The Mac version has been redesigned for macOS Sierra - and users will be able to enjoy document tabs when the new operating system ships later this year.

CrystalDiffract 6.6 resizable scroller thumb

Resizing the scroller thumb by clicking and dragging its
right-hand edge.

Tip: Taming the Scroller

CrystalDiffract's scroller view is like a smart scrollbar, complete with a preview of the full diffraction pattern:-

The scroller automatically appears whenever you scale or scroll. You can also make it appear by clicking one of the toolbar "Zoom" buttons. Note that, unlike previous versions, the Scroller now remains visible whenever the mouse pointer lies above the Scroller track.

Mineralogy of Uranium and Thorium

Robert Lauf's new textbook on uranium and thorium minerals makes excellent use of CrystalMaker® to bring crystal structures to life. The publishers have also licensed our CrystalViewer® software to provide fully-interactive exploration of the structures.

This colourful textbook is published by Schiffer Books and will be of interest to geologists, mineral collectors, as well as nuclear scientists and engineers interested in radioactive deposits.

CrystalViewer for Students

CrystalViewer icon

We provide CrystalViewer free-of-charge for individual student use. The software can be downloaded from our website and includes a built-in library of 100 structures, ready for instant display and measurement. CrystalViewer will also read from any CrystalMaker 9 file, meaning that you can share your structures with students, so they can improve their visual understanding "learning through play" in their own time, on their own machines.

Please note that CrystalViewer is not licensed for classroom use. We recommend purchase of a CrystalMaker site licence to allow the installation - and support - of multiple deployments of our software throughout your institution. By using licensed software, you help fund the further development of innovative software for scientific understanding. Thank you for your support!

CrystalViewer Textbooks

CrystalViewer is also available in bespoke editions, licensed by publishers to accompany textbooks in chemistry and mineralogy. Recent examples include Deer, Howie & Zussman's seminal An Introduction to the Rock-Forming Minerals, Klein & Philpotts' Earth Materials and Anthony West's Solid State Chemistry And its Applications. If you are interested in adding your title to the list, please feel free to contact us directly.

Tip: Add 3D Rotatable Models to iBooks

CrystalMaker 9 lets you export fully-rotatable 3D models which can be embedded into interactive textbooks - including Apple's new iBooks: a growing series of engaging learning resources. Simply export your structures as COLLADA 3D files, then drag-and-drop into Apple's excellent iBooks Author program for immediate display on Mac or iOS devices.

Exhibitions and Sponsorship

At the end of 2015 we sponsored the Royal Society of Chemistry's Solid State Group at their annual Christmas Meeting at the University of Kent, Canterbury. Shortly afterwards I travelled to Canterbury to host a CrystalMaker workshop for their Chemistry department. Crossing "The Pond", we exhibited at the American Chemical Society's Spring National Exposition in San Diego. This was followed, two weeks later, by the Materials Research Society's Spring National Exposition - the first to be held in Phoenix, Arizona. Both were very successful meetings and it was good to meet so many current (and new) CrystalMaker users - thank you to everyone who visited our booth!

More recently, we have sponsored the British Crystallographic Association's Spring meeting, the German Crystallographic Association's (DGK) annual newsletter, and a consortium of geochemical and mineralogical socities through advertising in their "Elements" magazine.

Tip: Simplify Complex Molecular Crystals

CrystalMaker's Selection > Make Polyhedron command isn't just for polyhedra! You can use this command to create a dummy atom at the centre of selection (without bonds), then use this dummy atom as a proxy for the entire molecule (whose sites can be hidden). This can be useful when working with simulations of molecular crystals, as you can focus on the relative positions of the individual molecules, without the visual overload of individual atoms and bonds.

Statement on "Brexit"

As many of you will know, the United Kingdom narrowly voted to leave the European Union. This non-binding referendum - with its knife-edge result - has led to a media frenzy; but at this stage, nothing is certain.

Please rest assured that whatever happens on the political stage, it remains "business as usual" here in Oxford. As a small, family-owned company, we aren't answerable to shareholders or at the mercy of international corporations, which leaves us free to do what we do best: developing and supporting our software for the benefit of our worldwide customer base.

Distance Explorer

Distance search around the Si "T1" site in the amphibole structure.
Histogram bars are colour-coded by element, so we can see that the
first-nearest-neighbour is oxygen (red) at ~1.6 Å

Tip: Distance Explorer

CrystalMaker 9 provides an interactive distance histogram, summarizing the range of distances around any specified site or element in the structure. This is akin to a "pair distribution function", but can be used as a quick way of assessing bonding in a new structure.

To display the Distance Explorer, choose: Measure > Distances (or click the Explore Distances button in the Bond Editor.)

Use the Distance Explorer's sidebar to customize your distance search by specifying the "from" and "to" sites or element symbols. You can explore the results in graphical or tabular form - and the window includes an Options menu with the option of graphics export.

Please note: you do not need to have generated bonds in order to use the Distance Explorer! The Explorer provides a handy way to assess possible bond distances prior to bond generation.

See us in Boston!

We shall be exhibiting at the Materials Research Society's Fall Meeting in Boston. The exhibition starts on Tuesday 29 November and ends after lunch on Thursday 1 December. See us in our usual location, on the main aisle, close to the Materials Town Square.

Vector Field in CrystalMaker 9

Magnetic dipoles associated with Mn
in a computer simulation (courtesy of
Martin Dove, QMUL).

Tip: Import Atom Vectors

CrystalMaker lets you import atom vector data from CrystalMaker "CMTX" text files. This is useful for visualizing vector fields - including simulation data. Very-large numbers of vectors can be defined in the text file, and then rapidly visualized in CrystalMaker.

The AVEC control card lets you specify a host atom, vector orientation, length, style and colour. This can be repeated for as many atoms as you wish (but you must ensure that you provide unique site labels).

For details on the formatting required - and examples - please see Appendix B in the CrystalMaker User's Guide (available from the program's Help menu).




Order Online and Save

If you're using older, unsupported versions of our software, please consider upgrading: you'll benefit from great new features, slick new interfaces, improved compatibility with the latest operating systems - and will be able to resume receiving free support and updates. Learn more about the great new features in CrystalDiffract 6.6 and CrystalMaker 9.2 for Mac and Windows.

If you order your upgrades online, you'll also benefit from our web discount which increases the more products you order (up to 20% off).

Tip: Synchronize Your Animations

CrystalMaker lets you assemble the frames of an animation or movie in the Views pane of the Overview window. You can animate the resulting sequence usign the Play command. Before you do this, however, you'll need to ensure that your individual views have the same scale, view direction, model type, etc. The Synchronize command is designed to automate this for you. However, for this to work, each structure must have the same set of site labels, otherwise CrystalMaker can't match sites from one structure to the next...


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