An integrated 'workbench' environment for Quantum Crystallography
Lead Research Organisation:
DURHAM UNIVERSITY
Department Name: Mathematical Sciences
Abstract
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| Description | We have created a fully functional platform which allows any participating crystallographic software to be part of a data pipeline. This enables meaningful crystallographic workflows while fully including any and all crystallographic software that chooses to be part of QCrBox. Concurrently, we have built the qcrtbx (quantum crystallographic toolbox) based on the cctbx (computations crystallographic toolbox). This significantly expands the capabilities of cctbx, one of the major computational platforms in the field, and forms a solid basis for future development. New crystallographic software can now be more easily developed based on cctbx/qctbx, which, given current developments in AI and Machine Learning, is highly relevant. This will lead to development based on existing 'tried and tested' routines, while being clearly structured and, crucially, instantly accessible to users through a common web browser interface. |
| Exploitation Route | The QCrBox will soon be populated with many and varied crystallographic software. Some of those (legacy software) will be given a 'new lease of life' because of the inclusion in the QCrBox, some will be current software packages and, curcially, it is now possible to 'capture' the myriad of small projects (by PhD Students and post-docs) in crystallographic laboratories worldwide. Currently, the vast majority of excellent 'hobby' projects simply disappear when scientists move on, but these can now be included in the QCrBox, and many of these will be highly valued in the future. All data interchange (internally and externally) is conducted via the Crystallographic Information File (CIF), an actively developed format officially mandated by the International Union of Crystallography (IUCr) and the Cambridge Structural Database (CCDC). The development undertaken within the QCrBox development has significantly contributed to meaningful extensions of the format, which will become part of the IUCr standards. |
| Sectors | Agriculture Food and Drink Chemicals Energy Environment Pharmaceuticals and Medical Biotechnology |
| URL | https://qcrbox.github.io/QCrBox/ |
| Description | The QCrBox will be used beyond the academic field of crystallography. In particular, pharmaceutical research will benefit from easy access to sophisticated refinement methods in an easy and structured, clean way that can be used securely within a secure intranet setting. On a different note, the QCrBox will enable educational institutions at all levels. An 'educational' version of the QCrBox can easily be put together and made available to interested parties. |
| First Year Of Impact | 2025 |
| Sector | Agriculture, Food and Drink,Chemicals,Education,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Description | Quantum Crystallography CIF dictionary working group |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Being able to report the results of new crystallographic techniques is essential to maintain the integrity of the field. |
| Description | Deep Learning-Accelerated Crystallography Pipeline |
| Amount | 17,477,886Â kr. (DKK) |
| Funding ID | NNF25OC0102835 |
| Organisation | Novo Nordisk |
| Sector | Private |
| Country | Denmark |
| Start | 01/2026 |
| End | 12/2030 |
| Title | Quantum Crystallography Toolbox (QCrBox) |
| Description | QCrBox (Quantum Crystallographic Toolbox) is a collaborative project transforming small-molecule crystallographic analysis. With a large and growing community of crystallographers and chemists, QCrBox provides the tools needed to make crystallography more accessible, reliable, and innovative for everyone. QCrBox has the full backing of major crystallographic institutions, including European and IUCr commissions on quantum crystallography, which recognise its potential to advance the field significantly. These official bodies, representing thousands of crystallography users worldwide, strongly advocate QCrBox's mission. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | QCrBox serves a broad international community of crystallographers, scientists, and software developers. Whether you're a seasoned researcher or new to the field, QCrBox provides tools that make it easier for everyone to participate in advanced crystallographic analysis. QCrBox's streamlined workflows, advanced methods, and reproducibility will benefit the growing user base. Researchers and developers are invited to contribute their own tools and software, with support from professional research software engineers who ensure sustainable integration. |
| URL | https://qcrbox.github.io/QCrBox/ |
| Description | Deep Learning-Accelerated Crystallography Pipeline |
| Organisation | Technical University of Denmark |
| Country | Denmark |
| Sector | Academic/University |
| PI Contribution | The now-completed QCrBox will form the basis for the extended pipeline to be built by Prof Anders Madsen in Copenhagen. This project can be seen as the direct successor of the QCrBox Project. I have not personally been part of the grant application, but I am a named collaborator/advisor for this work. The Durham team (Prof Norbert Pyerimhoff, Paul Niklas Ruth, and I) was heavily involved in the preparation of the grant application and was also present at the final presentation in the last funding round. I think it is safe to say that without the QCrBox (i.e., the outcome of this grant), the chances of this application being successful would have been greatly reduced. |
| Collaborator Contribution | While Prof Anders Madsen was a visiting Professor at Durham University, he and his research group were instrumental in providing steering and guidance during the construction phase of QCrBox. We could anticipate real-world requirements for the QCrBox, so that it is fit for purpose in building future crystallographic (X-ray, synchrotron and ED) pipelines. In the context of the above monetary discussion, I interpreted 'your research' as the QCrBox Project. This project can be seen as the direct successor of QCrBox, which will expand the existing project, ensure maintenance and continuation with a PhD student and a permanent member of staff at Durham University. |
| Impact | Prof. Madsen's project is about to commence. When it does (after the legal contracts are finalised), it will fund (1) Full-time PhD Student in the Department of Mathematics in Durham University (with Prof Norbert Pyerimhoff) (2) Three years of a full-time staff position based at Advanced Research Computing (ARC) at Durham University (Paul Niklas Ruth, the main architect of the QCrBox). |
| Start Year | 2026 |
| Description | Deep Learning-Accelerated Crystallography Pipeline |
| Organisation | University of Copenhagen |
| Country | Denmark |
| Sector | Academic/University |
| PI Contribution | Prof. Anders Madsen is a Visiting Professor at Durham University. He elected to spend a year there collaborating with the QCrBox project, bringing a Deep Learning (AI) aspect to the project while using the QCrBox's software integration capability and data management capabilities. Prof Madsen is at the forefront of using Deep Learning approaches in Crystallography and has significant ties to pharmacology and the pharmaceutical industries. Prof Madsen: https://researchprofiles.ku.dk/en/persons/anders-%C3%B8stergaard-madsen |
| Collaborator Contribution | This is an ongoing collaboration. Anders and his team in Copenhagen are currently working on the tight integration of their existing AI-related code with aspects of the QCrBox. |
| Impact | The first tangible outcomes are about to emerge as a tight integration of Prof Madsen's AI structure solution method (PhAI) with the QCrBox environment. We expect this to be available within a few months. |
| Start Year | 2024 |
| Description | Molecular Solid Solutions (MoSS): From Concept to Applications |
| Organisation | Durham University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The MoSS grant will make use of the QCrBox as well as the general Quantum Crystallographic knowledge we (OlexSys Ltd) hold. As such we are a named industrial partner to this grant UKRI2227. Withoug the QCrBox, this partnership would have been unlikely. |
| Collaborator Contribution | The project has just started. |
| Impact | No output yet |
| Start Year | 2025 |
| Title | QCrBox |
| Description | The QCrBox (Quantum Crystallography Box) is the core product to be developed during this award. The current version (March 2024) is an alpha developer release version. It is functional, and several sample applications are included. The documentation is up to a standard that knowledgeable developers and contributors can work with the software. |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | This product will keep all participating crystallographic software (contributions are open to all) under one umbrella. The QCrBox manages the data flow of the crystallographic data between the various participating software; installation can be local, in a local cloud or public clouds; access is via any standard browser. This will be the future of crystallography. |
| URL | https://github.com/QCrBox/QCrBox |
| Title | QCrBox |
| Description | The software is still under development. This is the declared outcome and purpose of the QCrBox Project. Please refer to the website at https://qcrbox.github.io/QCrBox/ |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | The software is still under development. Please refer to https://qcrbox.github.io/QCrBox/ |
| URL | https://qcrbox.github.io/QCrBox/ |
| Description | CECAM Discussion Meeting in Quantum Crystallography |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Simon Coles, Paul Niklas Ruth, and I were given one hour in this prestigious discussion group, where we presented the outcome of the QCrBox Project and led a discussion on the "Future of software design in Quantum Crystallography". Almost all the main 'players' in our small field were present, as were an international audience of ~30 early-career scientists. This highly esteemed discussion meeting was the perfect showcase for the QCrBox and coincided nicely with the end of the current grant period. |
| Year(s) Of Engagement Activity | 2026 |
| URL | https://www.cecam.org/workshop-details/3rd-cecam-discussion-meeting-on-quantum-crystallography-1370 |
| Description | Crystallography in Thailand |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | We visited various sites in Thailand (VISTEC, Thammasat, Chulalongkorn) and took part in (and ran a workshop) in a Chemistry Conference (STT50, Chiang Mai). The need of an integrated environment that provides access to standard crystallographic software as well as cutting-edge developments is clear. Participants engaged well with our projects and are looking forward to its final release. |
| Year(s) Of Engagement Activity | 2024 |
| Description | ECM Crystallography School Nancy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | We took part in the European Crystallography School, which was held in Nancy, France. We contributed lectures and a half-day workshop in which the QCrBox and its aim was presented. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://ecs-9.event.univ-lorraine.fr/ |
| Description | ICDM10 Conference Organisation |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | As a direct result of the QCrBox Project, Durham was chosen as the University where the European flagship conference for Quantum Crystallography was held. This conference happens every three years and was a major success. The QCrBox project was prominently presented and discussed at this conference, where the attendees formed the core user base, representing both users and developers of QCr software. |
| Year(s) Of Engagement Activity | 2026 |
| URL | http://www.icdm10.org |
| Description | IUCr Melbourne Workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We organised a QCrBox workshop at the General Assembly of the International Union of Crystallographers in Melbourne, Australia. We introduced the QuantumBox project to the main stakeholders in Quantum Crystallography and engaged with interested practising crystallographers. We engaged with the most important players and software authors during this workshop. In-depth discussions were held regarding the scope and direction the project is taking. This provided essential feedback for the future direction of the project (which was in it's first year a the point of the workshop) |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://iucr2023.org/workshops/ |
| Description | Participation in the Rigaku European User Meeting, New Isenburg, Germany |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | We presented and discussed the QCrBox concept in this European User Meeting of one of the major diffractometer manufacturers. The QCrBox project addresses many problems that are highly relevant to instrument providers and we are forging links for going forward with this. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Stall at ECM Conference, Padua |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We attended the European Crystallography Meeting in Padua, where we presented invited contributions and had an 'Industry Stall' where we presented the QCrBox project to the attendants of this important international Conference. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Talk at the BCA Spring Meeting Sheffield |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Niklas Ruth gave the first public talk at the British Crystallography Association Spring Meeting in 2023. The audience consisted of potential contributors to the box as well as future users. The concept was highly praised by the audience, and many discussions ensued. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Talk at the IUCr Conference in Melbourne |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A talk in a Quantum Crystallography session during the General Assembly of the International Union of Crystallographers in Melbourne, Australia. The Quantum Box project was introduced to an audience of practising crystallographers. A lively discussion followed the talk, and many offline discussions followed during the rest of the conference. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Workshop at 'Computer Fayre' during the IUCr Conference in Melbourne |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A hands-on workshop where the QuantumBox project was introduced practically. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Workshop at the Sagamore Charge Density Meeting, New Delhi, India |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Following the Sagamore International Charge Density Meeting (where we contributed two invited talks), we held a QCrBox workshop, where the concept of the project was communicated to this core target audience and a demo of the working system was provided. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.snu.edu.in/conferences/Sagamore2024/ |