The big news from October is that Rigaku Holdings Corporation, a global solution partner for X-ray analysis (headquarters: Akishima, Tokyo; president and CEO: Jun Kawakami), has completed its listing on the Tokyo Stock Exchange Prime Market. Rigaku Holdings is the parent company of the regional Rigaku sales and service offices in the Americas, Europe, Asia Pacific and China.
In other news, we held a ribbon-cutting at our new bioscience laboratory at SmartLabs in Cambridge, MA. The lab will be a technology demonstration center for the MoleQlyze, a tool for determining the electron density topography of proteins and other biomolecules in solution.
Left to right: Clement Fourney/SmartLabs, Jun Kawakami/Rigaku Holdings and Kent Heath/Rigaku Americas Holding Inc. cutting the ribbon.
Tamir Gonen, Mark Benson and I were interviewed as part of an article about MicroED appearing in Chemistry World.
Fraser has made the Rigaku School for Practical Crystallography available in an on-demand version. The school is available to anyone at any time. Details are found below.
We will be at AsCA2024 in Kuala Lumpur next week. If you are attending, please stop by our booth and see some of the new toys we’ve brought out this year.
Fraser provides our tip of the month on the use of Lattice-IT and Jeanette reviews Supremacy: AI, ChatGPT, and the Race that Will Change the World.
The results of last month’s survey suggest that half the respondents would come a rather long distance to visit us, while the other half think The Woodlands never has good weather. The summers can be brutal, but we do have year-round riding. 😊
We are pleased to announce the Rigaku School for Practical Crystallography (RSfPC) is now available as an on-demand course. You can access it at https://academy.rigaku.com 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. We started the school during the pandemic to try to fill the gap caused by the cancellation of many regional crystallographic teaching schools. The school was very well received and inspired us to keep it going over the last 4 years. Now we are offering the course via the web, on-demand to eliminate the issues many face with timezones and to extend the reach of the school further. I am very grateful to my colleagues who devoted significant energy and time to making the school a reality and providing a very high standard for the lecture content. We look forward to welcoming many new students with this new chapter in the story of 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.
Double the diffracted intensity, same operating costs
Maximizing the number of photons hitting your detector can make all the difference, whether you're clearing a backlog of samples or extracting data from a challenging one. The PhotonJetMAX-S, our latest microfocus sealed tube source for theXtaLAB Synergy-S, delivers more than twice the diffracted intensity while maintaining the versatility to handle a wide range of samples.
When designing the PhotonJetMAX-S, our goal was to enhance performance without increasing operating costs. The PhotonJetMAX-S uses the same tube technology as the PhotonJet-S, ensuring that when a replacement tube is needed, the cost remains the same. Additionally, it operates at the same power level as the PhotonJet-S, making it equally eco-friendly.
Enhanced performance
The PhotonJetMAX-S leverages Rigaku Innovative Technologies (RIT) optic technology to maximize photon capture from the tube and focus them onto the sample. Compared to the PhotonJet-S, it delivers over two times more photons to the detector.
Superior stability
Performance and stability go hand in hand. That's why the PhotonJetMAX-S is equipped with our water-to-air cooling approach. Our water-to-air cooling system uses water only where it’s necessary—in a closed, low-pressure circuit—to allow precise control of the source temperature and flux yet ensure reliability. Additionally, water efficiently removes heat from the cabinet eliminating the source as a cause of air turbulence and heat near the sample.
Proven reliability
Built with our long-life tube technology, the PhotonJetMAX-S is designed to keep running sample after sample for years, giving consistent performance and reliability.
Low operating costs
Operating the PhotonJetMAX-S won't break the bank. It uses the same tube technology as the PhotonJet-S, so replacement tubes are no more expensive. Plus, its low operating power keeps energy consumption—and your costs—down.
Eco-friendly design
The PhotonJetMAX-S achieves peak performance at just 50 W, making it the most energy-efficient, high-performance microfocus sealed tube system available.
By choosing the PhotonJetMAX-S, you’re enabling the analysis of smaller samples or increasing throughput as needed. With our patented divergence slits included as standard, you can confidently tackle any sample type, whether it has a large or small unit cell, is a single-crystal or powder, or is a twinned sample.
Crystals in the News
October 18, 2024
Nature interviewed Helen Berman, one of the founders of the Protein Data Bank, in recognition of the PBD’s contribution to the 2024 Nobel Prize in Chemistry.
Sometimes messy diffraction patterns obscure the periodicity of the expected unit cell(s). The Lattice-IT tool is a feature within Ewald explorer that allows the user to make selections based on periodicity so that the diffraction pattern can be cleaned up and thus more easily indexed. This also can be useful in separating diffraction patterns from different domains for twins or multi-crystals.
When to use it?
When you have diffraction patterns that cannot be easily indexed using automatic methods.
How to use it?
Figure 1: Lattice wizard showing the Ewald Explorer button.
First, open the Ewald Explorer tool from the lattice wizard. Once opened, you can reorient the diffraction pattern using left click and drag in the main window (Figure 2 green box) until you can see periodicity or you are looking down an axis of the unit cell. For a nice single crystal, this would look like a 2-D grid. To assist with this, you can use the view finder tool (Figure 2 purple box) to align along some predetermined orientations where CrysAlisPro has found reflection overlap.
Figure 2: The Ewald explorer window showing the “Selection/Lattice-IT” tool, the main view area (green box), the view finder tool (purple box) and how to activate Lattice-IT (red box).
Once you have a nice view, the Lattice-IT tool can be selected from the selections tab in EwaldExplorer and activated by selecting the radio button for Lattice-IT, (Figure 2 red box).
Next move the mouse cursor onto the main view window (Figure 3) and align the bar at the mouse cursor with any of the rows of reflections you can see that belong to the domain you are interested in. In the default mode, the tool will try to calculate the periodicity based on your mouse position. The overlaid dark bars (Figure 4) represent the detected periodicity, and the width of the dark bar indicates the tolerance. If you are satisfied, you can click to commit to the selection shown.
Figure 3: The Lattice-IT selection tool with the cursor bars lined up with a reflection row.
Figure 4: The Ewald Explorer window after committing a selection showing selection area bars as dark bars, selected reflections highlighted in green, adjustment tools (red box), assistance level (green box), the button to move selected reflections to another group (purple box) and the group summary with visibility selectors (orange box).
If you find the detected periodicity does not match your pattern, you can adjust the selection using the adjustment tools, using the options shown in Figure 4 (red box).
You can also hold the shift key to change the adjustment levels or for finer control when using the mouse to place the initial line.
The tool also allows different assistance levels that can be switched using the “find period, refine angle” dropdown and “Hints” checkbox, Figure 4 (green box).
Additional orientations may be added using the “New” button on the Lattice-IT tab, just above the adjustment tools, to define a 2D periodicity.
After clicking, reflections highlighted in green do not match the periodicity and can be moved to a different group using the “Move selected to…” option, shown in Figure 4 (purple box), on the “Selection/Lattice-It” tab leaving matching reflections in their initial group. In this manner, reflections can be easily filtered into groups representing different domains, or that do not match any domain.
Visibility of the groups can be manipulated using the checkboxes in the Group summary area, Figure 4 (orange box). Indexing can then be performed using visibility of reflections as a criterion, Figure 5.
Figure 5: Ewald explorer after hiding reflection group 2 and showing the option to index based on visibility accessed by clicking on the LATTICE option.
A typical workflow would be to place reflections only from domain 1 into group 1 and then make only group 1 reflections visible before indexing on visibility. For twins, the user would then make only group 2 reflections visible and add a twin domain by indexing on visible reflections once more (Figure 6).
Figure 6: Indexing a second domain using the Activate twin / multicrystal option with a second group of reflections.
Parmy Olson’s Supremacy: AI, ChatGPT, and the Race That Will Change the World is a quick read, but an important one. Clocking in at only 290 pages excluding notes and acknowledgements, Supremacy has the readability and accessibility of a typical beach read–which is a very good thing when the subject matter of the book is artificial intelligence (AI). AI is a buzzword right now. Since the new and improved ChatGPT 4 launched in March 2023, it seems like every major tech company has been throwing out its own versions of AI-powered tools–some better than others. The key takeaway from Olson’s Supremacy is fairly straightforward: AI is not a new technology, it has been around for a while in some form or another, and is certainly one that has taken years to hone and develop–although it is still far from perfect. The relative “newness” of AI is more a matter of public perception and accessibility of AI tools.
In Supremacy, Olson delves into two rival groups that worked to develop artificial generative intelligence (AGI): OpenAI and DeepMind. Software giant Microsoft owns the majority stake in OpenAI, and DeepMind is a subsidiary of Alphabet, Inc., a.k.a. Google. Both OpenAI and DeepMind started out more independently, only to essentially be absorbed by these larger corporations over time. The unfortunate outcome of these effective acquisitions is that what started out as two independent companies trying to create artificial general intelligence to broadly make the world a better place became something else entirely–and created an atmosphere of competition in Big Tech that should give anyone with an internet connection pause. AI is inevitable, and if you’ve been on the internet in your lifetime, you’ve already allowed major tech companies to mine your data and help train their AI models.
There is only so much Olson can tackle in 290 pages–and she does an excellent job of giving the reader a detailed introduction to the recent history of AI development and the rivalry between OpenAI and DeepMind. If she decides to write a follow-up, a guide to safely using AI, as well as a more in-depth analysis of its past, current, and future pitfalls vis-a-vis the safety of humanity, would be delightful to read.
