My neighbor of twenty-five years is a past chair of the Montgomery County (Texas) Republican Party. We are also good friends. We have differences of opinion, some strong, but we also agree on many topics; we just approach them from different points of view. He gave me a copy of Confronting the Presidents by Bill O'Reilly and Martin Dugard. I accepted with skepticism as I was expecting something rather unbalanced. The book was actually quite good and relatively balanced. I also learned a few things about some lesser-known US presidents. My point is that we should always keep an open mind and be respectful of our neighbors.
More sad news: George Sheldrick passed away last month and the crystallography community reeled with the news. The ACA has created a page for members to relate their memories of George: Remembering George Sheldrick. My last discussion with him was on the topic of SHELXT in 2015. I had told him I had spent more than an hour assigning 300+ atoms in a structure from successive difference Fourier maps. I decided to try SHELXT, submitted the data set and went for coffee. I told George that when I returned with my coffee, all the atoms had been assigned properly with the exception of some fluorines. He said, "I had to leave something for the crystallographers." George will be missed.
In this issue, Emilia Buchsteiner provides tips on dealing with incommensurate structures. Jeanette reviews Nexus this month. I added a video from Dr. Becky about the horizon problem in astrophysics—something to take your mind off daily events.
In this session, you will learn about the use cases of electron diffraction, success stories, challenges, and how they were overcome. Starting from the physical foundations and history of the technique, we will develop an outlook on what the future will bring to further push the boundaries of analytical insights unlocked by electron diffraction. Join us to see how ED is transforming research—register now!
The RSfPC is a course aimed at newcomers to crystallography and focuses on the practical aspects of crystallography with 10 lectures covering approx 10 hours and a course exam at the end.
The Rigaku School for Practical Crystallography was created during the pandemic to help fill the gap left by the cancellation of many regional crystallographic teaching schools. Thanks to the positive response over the past four years, it has continued to grow. Now offered on-demand, the course aims to make learning more accessible by overcoming time-zone challenges and reaching a wider audience.
We’re excited to welcome new students to the Rigaku School for Practical Crystallography.
Our LinkedIn groupshares information and fosters discussion about X-ray crystallography and SAXS topics. Connect with other research groups and receive updates on how they use these techniques in their own laboratories. You can also catch up on the latest newsletter or Rigaku Journal issue. We also hope that you will share information about your own research and laboratory groups.
Atrigakuxrayforum.comyou can find discussions about software, general crystallography issues and more. It’s also the place to download the latest version of Rigaku Oxford Diffraction’sCrysAlisProsoftware for single crystal data processing.
Dual-Wavelength Rotating Anode X-ray Diffractometer with HPC X-ray Detector
The ultimate single crystal X-ray diffractometer for a wide range of crystallographic applications
The introduction in 2004 of the Oxford Diffraction Gemini diffractometer, with two independent X-ray sources, was a watershed moment in crystallographic instrumentation. The groundbreaking design of the Gemini suddenly gave crystallographers the ability to easily switch between Cu and Mo wavelengths and greatly expanded the experimental flexibility available for analyzing single crystal samples. The XtaLAB Synergy-DW is an evolution of that revolutionary idea which retains the flexibility of the dual wavelength capability but in addition adds the exceptional flux enhancement of a reliable, rotating anode X-ray source. It is the perfect diffractometer for a core facility where protein crystallography and small molecule crystallography are both practiced.
Configuration
The XtaLAB Synergy-DW diffractometer contains a PhotonJet-R X-ray source that is based on the proven, low-maintenance MicroMax-007 HF microfocus rotating anode X-ray generator. The target is constructed with two different X-ray source materials (the following combinations are available: Mo/Cu, Cu/Cr, Cu/Co, Cu/Ag, and Ag/Mo) and is coupled with an auto-switching dual-wavelength optic. Two wavelengths of X-ray radiation are available at the click of a button and switching between wavelengths takes only 5 minutes. Rounding out the XtaLAB Synergy-DW configuration is the fast and efficient four-circle kappa goniometer which is coupled with Rigaku's Hybrid Photon Counting (HPC) X-ray detector, the HyPix-6000HE (or optionally the curved, large theta coverage detectors, HyPix-Arc 100° or HyPix-Arc 150°.) which has essentially no readout noise, no dark noise and high dynamic range. All of this controlled by the CrysAlisPro diffraction software package with sophisticated algorithms to tie the hardware together to minimize the time it takes to measure and solve single crystal X-ray structures.
Proven reliability
The PhotonJet-R source was designed with reliability in mind. Clever Rigaku engineering makes filament changes easy, like swapping a printer cartridge, with no need to realign the source each time. Scheduled maintenance involves one annual visit from a Rigaku engineer, as with all XtaLAB Synergy diffractometers, and typically takes 1-2 days. With the anode exchange program, you get the benefit of rotating anode power with the convenience of sealed tubes.
Beam conditioning
Where overlapping peaks are a concern, e.g. large unit cells, proteins, twinned or incommensurate lattices, high beam divergence is undesirable. On PhotonJet sources, a software controlled, motorized variable beam slit is available as an option to alter divergence to adapt the source to your sample's requirements. For those samples where intensity matters most, the slit can be fully opened giving the highest flux. For those where peak sharpness and overlap are factors, the beam can be limited to a divergence anywhere between 1 to 10 mrad.
CrysAlisPro
The XtaLAB Synergy-DW comes complete withCrysAlisPro, our user-inspired data collection and data processing software for single crystal analysis. Designed around an easy-to-use graphical user interface, CrysAlisPro can be operated under fully automatic, semi-automatic or manual control. CrysAlisPro combines automated crystal screening, the fastest and most accurate strategy software available, concurrent data reduction and automatic small molecule structure solution. CrysAlisPro can operate either in a protein or small molecule dedicated workflow. Popular third-party protein data processing packages can easily process diffraction data if desired. Visual feedback is provided for each step with clear, color-coded guidance so that both novices and experts can collect high-quality data in the shortest time possible.
AutoChem
AutoChem is the ultimate productivity tool for small molecule chemists, offering fast, fully automatic structure solution and refinement during data collection. Developed in collaboration with OlexSys Ltd (Durham University, UK), AutoChem works in conjunction with Olex² where more advanced structure solution and refinement functionality exists. AutoChem is seamlessly integrated within CrysAlisPro, and forms an integral part of our 'What is this?' feature. The 'What is this?' feature gives you structures quickly and ensures you are not wasting time collecting full datasets on known samples or starting materials. It is an alternative pre-experiment option, which is used to plan your full data collections.
Rigaku offers a crystal structure determination service with scientific support, with data collection on a XtaLAB Synergy-ED diffractometer in Rigaku's own laboratories.
Access our electron diffraction service delivering all structural information, datasets, raw data files and software to re-process at your own leisure. Electron diffraction can be carried out on samples with crystallites under 1 micron in size, meaning that crystallization trials for traditional X-ray analysis no longer have to become a bottle neck to structural analysis.
Useful tools for incommensurate structure analysis
For structures with incommensurate modulation, it is recommended to use 3D peak extraction via the "Peak hunting with user settings" tab to obtain the most accurate peak positions (Figure 1).
Figure 1: Peak hunting with user settings tab. Select peak hunting with 3D peak positions.
In the next step, one needs to determine the unit cell by indexing the main reflections. For incommensurate structures, automatic unit cell finding often only yields a supercell. Alternatively, the cell parameter range can be adjusted by limiting the maximum value of a user cell in the "Custom unit cell finding" tab (Figure 2).
Figure 2: Custom unit cell finding tab. Select a user cell and adjust the max. value to the range of your desired cell parameters.
As another option, filters can be applied to only show the strongest reflections, as satellite reflections are typically much weaker than main reflections (Figure 3). Afterwards, "Automatic unit cell finding in shown peaks" can be used.
Figure 3: (left) Ewald Explorer showing all reflections including satellite reflections. (right) Ewald Explorer showing only the strongest reflections. With most satellite reflections filtered out, the unit cell is clearly visible.
Once the correct unit cell is identified, the next step is to define the q vector. To improve the visibility of the satellite reflections, it can be helpful to switch to collapsed view in Ewald Explorer, which folds reciprocal space onto the specified number of cells (Figure 4). The pink crosses indicate the positions of the satellites based on the current q vector.
Figure 4: Collapsed view in Ewald Explorer.
To add a modulation vector, incommensurate peak options have to be switched on (Figure 5, red box). Editing the q vector is enabled by double clicking on it (Figure 5, green box). Start by adding a single order and entering the estimated coordinates of the vector before refining the unit cell with satellites (Figure 5, blue box). Continue adding orders until all reflections are properly described. If this is not possible, it may indicate that a second modulation vector is needed, the unit cell is incorrect, or the structure might not be incommensurate after all. To view additional information about the satellites, check the box next to "Log window" after refining the satellites. This will display the numbers of reflections assigned to each satellite order. They can also be seen at the bottom of the "Crystal" tab (Figure 5, yellow box). Only use orders up to the point where there are still reflections assigned to them.
Figure 5: Crystals tab. Red box: add one (or more) q vector(s). Green box: Click on the q vector to open a window where you can edit the q vector and the order of the satellites to be taken into account during refinement. Blue box: Refine the unit cell with satellites. Yellow box: Information about the amount of indexed main and satellite reflections.
Once a modulation vector is added, the selection groups will automatically generate a tab where you can toggle the satellite reflections on and off (Figure 6).
Figure 6: (left) Satellite reflections are shown. (right) Satellite reflections are hidden. The position of the satellites based on the determined modulation vector is indicated by the pink crosses.
If the modulation vector was refined, a single q vector, along with the assigned orders in Ewald Explorer, will be automatically selected during data reduction. If there are multiple q vectors, generate the reduction list by selecting "Other (reduction list)" first, then proceed with data reduction (Figure 7).
Figure 7: Data reduction workflow. For incommensurate structures, a single q vector is automatically selected for data reduction. For more than one q vector, "Other" has to be selected to generate a reduction list.
Finally, the data has to be refinalized to include the hkl values in the .cif file via the export options (Figure 8). Then it can be imported into Jana2006/2020 for super space group determination and structure solution.
Figure 8: Refinalization of the dataset. By clicking "Export options" a window opens, where a .cif export with hkl can be selected.
Scientists from the Czech Republic and Japan have used diffraction methods to study a lightweight titanium shape-memory alloy that functions in a broad temperature range.
February 27, 2025
Researchers from Romania and the US have synthesized and characterized berkelocene.
Video of the Month
The Horizon Problem | The Universe's biggest UNSOLVED mystery
Yuval Noah Harari's latest book, Nexus: A Brief History of Information Networks from the Stone Age to AI, is a hefty read at 404 pages, excluding the nearly 100 pages of notes and indices. However, each of the book's only eleven chapters is split into smaller semi-self-contained chunks, marked by a subheading. This makes digesting the ambitious book much easier.
As the subtitle suggests, Nexus is a historical investigation of information networks from the earliest days of humanity to the present—with many predictions and concerns about what the future holds, given the prolific rise of artificial intelligence (AI) and its potentially damaging effects on information networks around the world.
In Part I, Harari starts at the beginning, detailing the evolution of human networks from word-of-mouth to the printing press and beyond. In Part II, Harari delves into the rise of the computer and the digital information age. And in Part III, he addresses the broader societal and political impacts of our computer-dependent world in the age of AI.
Harari expresses trepidation regarding the prevalence of AI in our modern world. He methodically illustrates the dangers of misinformation and disinformation networks to human society over and over again, with historical example after historical example. From ancient Rome to Nazi Germany to modern-day America, he provides insightful anecdotes that only prove the frequency with which history tends to repeat itself.
Nexus is, at times, a hard book to read—not because it is not well-written, as Harari's prose is masterful—but because the subject matter is challenging to accept.
