November 2025 - ChimeraX-users - RBVI Mailing Lists

color of capped surface
by stokes＠nyu.edu 12 Nov '25

12 Nov '25

I am having trouble with the surface color and specifically of capped surfaces. To start, surfaces of individual chains are given a single color, despite individual domains having been assigned a variety of colors. I can change the colors of the surface for individual domains subsequently, so that is not so bad. However, the color of the capped surface remains the initial color adopted when the surface was created. When I change colors of the individual chains, or domains, the surface color changes, but not the color of the capped/clipped surface. If I change the color of the entire model, then the surface cap changes. But it does not respond to subsequent changes of individual chains and domains. Hiding/showing the surface does not solve the problem (though I have a dim memory of this working in the past - maybe that was the old chimera). I am only using near/far clipping planes - not front/back. ChimeraX 1.10.1 on Ubuntu and 1.8 on Windows behave the same. Thanks in advance for any insight, David

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Blurry Volume Rendering in ChimeraX ≥1.7 on macOS (HiDPI Regression Affecting ArtiaX)
by Yaroslav Tsytsyura 11 Nov '25

11 Nov '25

A little comment to the message: The following text was generated with help of an AI, because I’ve got frustrated trying to solve the issue myself and ran out of strength; I apologise for that. Yet it describes the problem well: Dear ChimeraX/ArtiaX developers, I would like to report an issue with volume rendering quality on macOS that appears to have been introduced in ChimeraX versions 1.7 and later, and that affects ArtiaX-based tomography workflows. System details macOS 26.0.1 on Apple Silicon (M2 Pro; RAM 16GB) ChimeraX 1.6.1 (works correctly) ChimeraX 1.7–1.10.1 (affected) ArtiaX 0.3 (works correctly) ArtiaX 0.6 (affected) Native ARM64 ChimeraX binary used (not via Rosetta) Tested both on the built-in display and external 4K monitor Issue summary When displaying reconstructed tomograms (binned 4x to pixel value 10A) in ChimeraX 1.7 and newer, the volume appears blurry, pixelated, and significantly lower in resolution compared to Fiji or ChimeraX 1.6.1. The same tomogram, same hardware, same display settings, and same scaling factors show correct high-quality sampling in ChimeraX 1.6.1 + ArtiaX 0.3. In contrast, ChimeraX ≥1.7 + ArtiaX ≥0.6 consistently produce a downsampled-looking rendering. Troubleshooting performed To rule out common macOS/Qt/HiDPI issues, I have tested: Forcing HiDPI mode (QT_ENABLE_HIGHDPI_SCALING, QT_SCALE_FACTOR, etc.) Launching via arch -arm64 Removing and reinstalling ChimeraX completely (including preferences) Disabling external 4K monitor scaling Resetting ChimeraX user settings None of these affected the outcome. Only reverting ChimeraX to version 1.6.1 restores correct rendering quality. Behavior differences observed In ChimeraX 1.6, tomograms appear crisp and match Fiji’s display quality. In ChimeraX 1.7–1.10.1, the same tomograms appear visibly blurred and pixelated. The command graphics quality high or similar parameters appear unsupported or ineffective in newer versions. ArtiaX toolbar loads but seems to use lower-resolution textures for slice volumes. This strongly suggests a rendering pipeline change around the transition from ChimeraX 1.6.1 → 1.7 that affects ArtiaX’s volume display on macOS (possibly due to Qt scaling, offscreen framebuffer size, or texture sampling changes). Request Could you please check whether: ArtiaX 0.6 is triggering half-resolution internal textures on macOS? The new rendering pipeline introduced in ChimeraX ≥1.7 affects HiDPI texture sampling? There is a fallback path on macOS ARM that reduces framebuffer resolution? Any configuration options can restore full-resolution sampling? To illustrate the difference between the two options (ChimeraX 1.6 vs 1.10.1) I have included the snapshots from two different M2 MacBooks running two different versions of ChimeraX/ArtiaX combinations; the tomogram file, tomogram optical slice position are the same, the screen magnification and the regions displayed are very similar. Thank you very much for your work and for looking into this. Best regards, Yaroslav ------------------------------------------- Dr. Yaroslav Tsytsyura Cellular Biophysics Institute of Medical Physics and Biophysics University of Muenster Robert-Koch Str., 31 48149, Muenster GERMANY phone: +49 251 8351 010 fax: +49 251 8355 121 Mobile: +49 157 895 47789 web-page: https://www.medizin.uni-muenster.de/impb/das-institut/elektronenmikroskopie…

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Offscreen/headless render acceleration
by Roden Deng Luo 07 Nov '25

07 Nov '25

Hi, In https://www.cgl.ucsf.edu/chimerax/docs/user/options.html, under `--offscreen`, it says "It cannot use a graphics card or hardware-accelerated rendering because OpenGL does not support rendering without a window." I wonder if there are any possible ways to utilize graphics cards in the headless mode, or if you have any best practices for saving pictures/movies for hundreds to thousands of structures, with or without a GUI. Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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front-back shadow
by Citterico, Matteo 07 Nov '25

07 Nov '25

Hello, I’m having trouble changing the depth cue start and end settings in ChimeraX 1.8. I’ve tried several commands, but none of them seem to work. Could you please help me with this? Thank you in advance, Matteo

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Recent spam
by Eric Pettersen 06 Nov '25

06 Nov '25

It seems that the era of AI bots signing up for and posting to mailing lists is upon us. I have banned the email address of the recent spam source and we are investigating methods to prevent these kinds of sign-ups/posts in the future. --Eric Eric Pettersen UCSF Computer Graphics Lab

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The House Always Wins
by johncarry9t＠gmail.com 06 Nov '25

06 Nov '25

The word "casino" conjures specific imagery: the clinking of chips, the hypnotic spin of the roulette wheel, the electric chorus of a slot machine jackpot. For centuries, these establishments have been temples of chance, promising glamour, excitement, and the life-changing possibility of a big win. But behind the flashing lights and free-flowing cocktails lies a meticulously engineered ecosystem designed for one ultimate goal: profitability. The modern casino is a fascinating blend of psychology, architecture, technology, and entertainment, far removed from the smoky, simplistic gambling halls of the past. https://hamiltongardens.org/visit/ The Architecture of Addiction: Designed to Disorient From the moment you step inside, the casino environment is carefully crafted to keep you playing. There are no clocks or windows, creating a timeless bubble where the outside world ceases to exist. Labyrinthine floor plans encourage exploration and make it difficult to find the exit. The air is oxygenated to keep patrons alert, and the constant sensory stimulation—from the ringing of slots to the vibrant carpet patterns—creates an atmosphere of thrilling chaos. This design is no accident. It's a calculated strategy to maximize "time on device." The longer a guest stays, the more the mathematical advantage of the games, known as the "house edge," grinds down their bankroll. Every element, from the placement of popular slots to the complimentary "comps" like drinks and hotel rooms, is a tool to enhance customer retention. The Games: A Calculated Dance of Chance At its core, a casino's business model is a masterpiece of applied mathematics. Every game offered is statistically tilted in the house's favor. Slot Machines: The undisputed king of the casino floor, slots are now sophisticated computers. Their outcomes are determined by Random Number Generators (RNGs), and their payout percentage, or "Return to Player" (RTP), is programmed in advance. Their appeal lies in their simplicity and the potential for massive, albeit infrequent, jackpots. Table Games: Games like Blackjack, Roulette, and Baccarat offer more player agency, but the house edge is immutable. In Blackjack, the dealer plays by fixed rules that disadvantage the player over time. In Roulette, the presence of the "0" and "00" on the American wheel gives the house its built-in advantage. Craps and Baccarat operate on similar statistical principles. Despite the odds, these games thrive because they offer the illusion of control and the social spectacle of a live game, presided over by a skilled dealer. Beyond the Floor: The Rise of the Integrated Resort The 21st-century casino is rarely just a casino. The model of the "Integrated Resort" has transformed these venues into full-scale entertainment destinations. Today's major casinos are home to: World-class hotels and spas Celebrity-chef restaurants High-end retail shopping Arena-sized theaters hosting A-list performers Convention and meeting spaces This diversification is a strategic move. By attracting conventioneers, gourmands, and concert-goers who may not be primary gamblers, resorts ensure a steady revenue stream that isn't solely dependent on the volatility of the gaming floor. It normalizes the casino, repositioning it as a legitimate vacation spot for a broader demographic. The Digital Frontier: Online Casinos and the Future The most significant shift in recent years has been the explosive growth of online casinos and mobile sports betting. The digital realm removes all physical barriers, allowing people to gamble from their living rooms or on their phones. This presents both immense opportunity and significant challenges. Online platforms use sophisticated algorithms and bonus structures to engage players, often with even higher efficiency than their brick-and-mortar counterparts. This accessibility has intensified the focus on responsible gambling. Regulators and ethical operators are now implementing tools like deposit limits, "cool-off" periods, and self-exclusion programs to help mitigate the risks of addiction that are amplified in the always-available online environment. The Final Bet The modern casino is a complex entity. It is a source of employment, tourism revenue, and entertainment for millions. It is also a highly engineered environment that profits from human psychology and mathematical certainty. As the industry continues to evolve with technology and expand into new markets, the balance between entertainment, profit, and social responsibility remains its defining tension. The house may always win in the end, but understanding the intricate machinery behind the magic curtain is the most valuable bet a visitor can make.

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F8BET Payment Methods
by johncarry9t＠gmail.com 06 Nov '25

06 Nov '25

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confirm
by 汪洋 05 Nov '25

05 Nov '25

 confirm c28d09cf0893ee23fc780e120106b9b266ea0623

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ChimeraX VR (specifically LookSee)
by jrj.healey＠gmail.com 02 Nov '25

02 Nov '25

Hi all, I'm trying to get ChimeraX VR standalone working on a Quest 3. Trying to follow the instruction online, but I fall at pretty much the first hurdle trying to subscribe to the release candidate channel on Meta AppLab - I get an error saying the channel is out of date or can no longer be found (or something to that effect). Do you have any more information on this, and does this mean side-loading is my only option potentially? Thanks Joe

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What is the University of Michigan manufacturing partnership with LS Manufacturing?
by altabunny9_at_gmail.com＠mail.d2l.msu.edu 01 Nov '25

01 Nov '25

In today’s rapidly evolving industrial landscape, the manufacturing sector stands at the intersection of innovation and technology. From 3D printing (additive manufacturing) to CNC machining (subtractive manufacturing), modern engineers are required to bridge the gap between theory and real-world application. Recognizing this growing need, the University of Michigan’s College of Engineering has established a ground-breaking partnership with LS Manufacturing, a leading global on-demand manufacturing company. This collaboration—centred around the University of Michigan manufacturing partnership initiative—aims to provide students with hands-on experience in additive and subtractive manufacturing education, bridging academic theory with real-world industrial practices. Together, they are shaping the next generation of manufacturing engineers, innovators, and entrepreneurs. <ol> <li>Introduction</li> </ol> Manufacturing today is not just about producing parts; it’s about producing ideas, efficiency, and sustainability. The rise of additive manufacturing technologies such as 3D printing, alongside traditional subtractive manufacturing methods like CNC machining, has transformed how engineers design, test, and create. Yet, one challenge remains constant in academia—how can students gain real-world manufacturing experience before entering the workforce? Hands-on education is crucial to understanding how concepts like material tolerances, design for manufacturability (DFM), and prototyping translate from theory into production. To address this, the University of Michigan Engineering Department, in partnership with LS Manufacturing, launched a forward-thinking initiative to blend classroom learning with industrial collaboration. This partnership emphasizes rapid prototyping for academic research, student project sponsorship in CNC machining, and opportunities for real-world manufacturing experience for students through capstone project sponsorships and innovation-focused technical grants. <ol start="2"> <li>The Partnership’s Vision & Goals</li> </ol> The University of Michigan manufacturing partnership with LS Manufacturing was born from a shared vision: to cultivate a new generation of engineers fluent in both the digital and physical realms of production. Goal 1: Enhance Student Learning At its core, the partnership focuses on improving how students learn and apply manufacturing principles. By providing access to industrial-grade manufacturing equipment, students can design, prototype, and refine projects using professional tools like high-precision CNC machines and advanced 3D printers. This approach transforms the University of Michigan’s classrooms and labs into dynamic, industry-connected learning environments. Students don’t just learn about manufacturing—they experience it firsthand. Goal 2: Bridge Theory and Practice Engineering theory provides the foundation for design, but practice makes it meaningful. Through this partnership, students engage directly with industry partners from University of Michigan Engineering and LS Manufacturing experts. They receive practical insights into design for manufacturability (DFM), rapid prototyping, and low-volume production—critical skills that align with modern industry expectations. For instance, when developing prototypes, students can leverage rapid prototyping for academic research, gaining experience in both additive and subtractive processes. This real-world engagement ensures they are not only technically proficient but also ready to innovate efficiently. Goal 3: Foster Innovation Innovation thrives at the intersection of creativity and capability. The University of Michigan partnership supports student-led initiatives such as the Solar Car Team, Robotics Club, and Formula SAE by providing manufacturing expertise, technical feedback, and production services. From concept sketches to final assembly, LS Manufacturing’s involvement helps these teams iterate faster and smarter. This collaboration empowers students to push the boundaries of engineering innovation while gaining the confidence to lead future industry breakthroughs. <ol start="3"> <li>How the Partnership Works: The “LS Manufacturing Technical Grant”</li> </ol> At the heart of this collaboration lies the LS Manufacturing Technical Grant, a unique sponsorship-in-kind program designed to empower student innovation. Through this grant, LS Manufacturing offers selected University of Michigan student projects and faculty research initiatives a combination of expert DFM feedback, rapid prototyping services, and production support using state-of-the-art CNC machining, 3D printing, and injection molding technologies. This model represents a corporate sponsorship in manufacturing that prioritizes educational value and accessibility. Rather than a traditional cash grant, it provides students with tangible, high-impact resources—professional-grade components, real-time consultation, and access to global production networks. Application Process The process is simple and inclusive. Student teams, faculty members, or research labs can apply through the University of Michigan Engineering Department’s partnership portal. Applicants outline their project goals, design needs, and desired manufacturing processes. Selected participants receive LS Manufacturing’s technical support to bring their designs to life. This initiative promotes student project sponsorship in CNC machining and similar technologies, encouraging students to prototype and test ideas efficiently. It’s a hands-on, learning-by-doing opportunity that merges academic ambition with industrial capability. <ol start="4"> <li>Expected Impact & Benefits for UM Students</li> </ol> The collaboration’s impact extends far beyond the classroom. It delivers a transformative learning experience by combining advanced technology, mentorship, and real-world exposure. Access to Global Manufacturing Networks Through LS Manufacturing’s online instant quoting platform, students gain access to a vast global manufacturing network. They can upload designs, receive cost estimates instantly, and understand how design choices affect pricing and feasibility. This mirrors real-world industry practices, preparing them for professional engineering roles where digital manufacturing tools are essential. Reduced Project Costs and Lead Times Student projects often face challenges such as limited funding and long turnaround times. LS Manufacturing helps address both issues by providing cost-effective production support and faster lead times. Whether it’s producing a prototype for a capstone project or components for research testing, students can move from concept to prototype at record speed. Skill Development and Industry Interaction Beyond technical proficiency, this partnership develops professional skills—teamwork, communication, and project management. Students interact directly with LS Manufacturing’s engineering experts, gaining feedback on design feasibility and manufacturing optimization. Such exposure provides a window into real-world manufacturing experience, helping them bridge the often-cited gap between academia and industry. Accelerated Research and Innovation For faculty and graduate researchers, access to LS Manufacturing’s rapid prototyping services means faster testing and iteration cycles. Projects that once took months to prototype can now progress in weeks, enabling researchers to focus more on innovation and less on logistical barriers. Ultimately, this partnership enhances not just student outcomes, but the entire research ecosystem at the University of Michigan. <ol start="5"> <li>About LS Manufacturing</li> </ol> LS Manufacturing is a global leader in on-demand manufacturing and rapid prototyping services, empowering innovators and engineers to move from prototype to production with speed and precision. Their core capabilities include CNC machining, 3D printing, injection molding, and sheet metal fabrication—making them a one-stop solution for any stage of the manufacturing process. Through collaborations with academic institutions, LS Manufacturing demonstrates its commitment to supporting education, innovation, and workforce development. By working with the University of Michigan, the company is investing in the future of engineering talent and helping shape the next generation of manufacturing leaders. To learn more about their services and mission, visit <a class="external" href="http://www.lsrpf.com" target="_blank" rel="noreferrer noopener">www.lsrpf.com</a>. <ol start="6"> <li>Conclusion & Looking Ahead</li> </ol> The partnership between the University of Michigan and LS Manufacturing exemplifies what’s possible when academia and industry work hand in hand. By merging additive and subtractive manufacturing education with real-world applications, the collaboration equips students with the tools, experience, and confidence to lead the future of manufacturing. Through the LS Manufacturing Technical Grant, University of Michigan students are not only designing innovative products but also learning how to manufacture them efficiently—a skill set that’s indispensable in the global economy. As this partnership continues to grow, it promises to inspire new research collaborations, support entrepreneurial initiatives, and redefine how engineering education meets the demands of modern manufacturing. The future of the industry depends on creative thinkers, hands-on problem solvers, and innovators—and this program ensures they’re ready to lead. <ol start="7"> <li>Call to Action (For the UM Audience)</li> </ol> Faculty and student teams interested in exploring manufacturing innovation or applying for the LS Manufacturing Technical Grant are encouraged to contact the University of Michigan College of Engineering Department of Mechanical Engineering or visit the UM Engineering Partnership Page for more information. This is more than a sponsorship—it’s a movement toward redefining how students learn, design, and build. Together, the University of Michigan and LS Manufacturing are crafting the future of engineering education—one prototype at a time. FAQs <ol> <li>What is the University of Michigan manufacturing partnership with LS Manufacturing?</li> </ol> The University of Michigan manufacturing partnership with LS Manufacturing is a collaborative program designed to give students hands-on experience in modern manufacturing technologies. It combines additive (3D printing) and subtractive (CNC machining) education, helping students bridge the gap between classroom learning and real-world industrial practice. <ol start="2"> <li>How does the LS Manufacturing Technical Grant benefit University of Michigan students?</li> </ol> The LS Manufacturing Technical Grant provides selected students and faculty projects with in-kind sponsorship. This includes DFM (Design for Manufacturability) feedback, rapid prototyping services, and production support using advanced manufacturing technologies. It reduces project costs, shortens lead times, and gives students direct access to industry-level expertise. <ol start="3"> <li>Who can apply for the LS Manufacturing Technical Grant at the University of Michigan?</li> </ol> The grant is open to University of Michigan students, faculty members, and research teams involved in academic or innovation-based projects. Applications can be submitted through the University of Michigan Engineering Department’s partnership portal, detailing project goals and manufacturing requirements. <ol start="4"> <li>What kind of real-world experience do students gain through this partnership?</li> </ol> Students gain real-world manufacturing experience by collaborating directly with LS Manufacturing engineers, learning about design for manufacturability, rapid prototyping, and low-volume production. They also gain exposure to digital tools like instant quoting platforms and online manufacturing networks, preparing them for careers in modern industry. <ol start="5"> <li>How can faculty or student teams learn more about the LS Manufacturing partnership?</li> </ol> Interested participants can visit the University of Michigan College of Engineering’s Partnership Page or contact the department directly for detailed program information. The page includes application guidelines, eligibility details, and examples of past capstone project sponsorships supported by LS Manufacturing.

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