Jon Agirre
@glycojones.bsky.social
YSBL, Department of Chemistry, University of York, UK. I make, modify and fix stuff. Acta Cryst F main editor with Mark and Cristy. CCP4wg2 chair with Arnaud. Analyse glycan structures with Privateer: https://privateer.york.ac.uk #RealTimeChem [He/Him]
Pinned
Jon Agirre
@glycojones.bsky.social
· Sep 24
Structure of Plasmodium vivax N-myristoyltransferase with the NMT inhibitor IMP-1088
YouTube video by International Union of Crystallography
www.youtube.com
I'm incredibly proud to present this @actacrystf.iucr.org interview with Alex Mendez and Cydni Bolling on their first paper ever! The interview was co-led by Dr Graham Chakafana from Hampton University in the USA, who supervised the authors' undergraduate research.
www.youtube.com/watch?v=5rjI...
www.youtube.com/watch?v=5rjI...
One of the coolest things going on here is that the GitHub repos contain Jupyter notebooks for you to try their software. In case you don't have Jupyter installed or don't know what it is: you can always upload the notebooks to Google Colab and run everything on their cloud services :)
Tools are presented that are useful for collating existing public cryoEM data sets and/or creating new synthetic cryoEM data sets to aid the development of novel data processing and interpretation algorithms #CryoEM #ElectronCryomicroscopy #Python doi.org/10.1107/S205...
October 22, 2025 at 3:58 PM
One of the coolest things going on here is that the GitHub repos contain Jupyter notebooks for you to try their software. In case you don't have Jupyter installed or don't know what it is: you can always upload the notebooks to Google Colab and run everything on their cloud services :)
Great to see this article by @guptapenn.bsky.social is out! Kushol helped us interview @xtalmaker.bsky.social Vivian Stojanoff and @gabbygrowsxtals.bsky.social who published an article on careful sample preparation in crystallisation experiments, also part of #SAMPREP
www.youtube.com/watch?v=m34R...
www.youtube.com/watch?v=m34R...
October 10, 2025 at 10:07 AM
Great to see this article by @guptapenn.bsky.social is out! Kushol helped us interview @xtalmaker.bsky.social Vivian Stojanoff and @gabbygrowsxtals.bsky.social who published an article on careful sample preparation in crystallisation experiments, also part of #SAMPREP
www.youtube.com/watch?v=m34R...
www.youtube.com/watch?v=m34R...
Reposted by Jon Agirre
I'm incredibly proud to present this @actacrystf.iucr.org interview with Alex Mendez and Cydni Bolling on their first paper ever! The interview was co-led by Dr Graham Chakafana from Hampton University in the USA, who supervised the authors' undergraduate research.
www.youtube.com/watch?v=5rjI...
www.youtube.com/watch?v=5rjI...
Structure of Plasmodium vivax N-myristoyltransferase with the NMT inhibitor IMP-1088
YouTube video by International Union of Crystallography
www.youtube.com
September 24, 2025 at 4:31 PM
I'm incredibly proud to present this @actacrystf.iucr.org interview with Alex Mendez and Cydni Bolling on their first paper ever! The interview was co-led by Dr Graham Chakafana from Hampton University in the USA, who supervised the authors' undergraduate research.
www.youtube.com/watch?v=5rjI...
www.youtube.com/watch?v=5rjI...
I'm incredibly proud to present this @actacrystf.iucr.org interview with Alex Mendez and Cydni Bolling on their first paper ever! The interview was co-led by Dr Graham Chakafana from Hampton University in the USA, who supervised the authors' undergraduate research.
www.youtube.com/watch?v=5rjI...
www.youtube.com/watch?v=5rjI...
Structure of Plasmodium vivax N-myristoyltransferase with the NMT inhibitor IMP-1088
YouTube video by International Union of Crystallography
www.youtube.com
September 24, 2025 at 4:31 PM
I'm incredibly proud to present this @actacrystf.iucr.org interview with Alex Mendez and Cydni Bolling on their first paper ever! The interview was co-led by Dr Graham Chakafana from Hampton University in the USA, who supervised the authors' undergraduate research.
www.youtube.com/watch?v=5rjI...
www.youtube.com/watch?v=5rjI...
Reposted by Jon Agirre
The World Directory of Crystallographers (WDC) offers an unparalleled compilation of expertise in the field.
It’s free to join and open to all crystallographers and other scientists employing crystallographic methods.
Add your name and be part of the mosaic:
🔗 www.iucr.org/people/wdc
It’s free to join and open to all crystallographers and other scientists employing crystallographic methods.
Add your name and be part of the mosaic:
🔗 www.iucr.org/people/wdc
September 12, 2025 at 1:05 PM
The World Directory of Crystallographers (WDC) offers an unparalleled compilation of expertise in the field.
It’s free to join and open to all crystallographers and other scientists employing crystallographic methods.
Add your name and be part of the mosaic:
🔗 www.iucr.org/people/wdc
It’s free to join and open to all crystallographers and other scientists employing crystallographic methods.
Add your name and be part of the mosaic:
🔗 www.iucr.org/people/wdc
Reposted by Jon Agirre
Just a few days left to register for the next Diamond/CCP4 Data Collection and Structure Solution Workshop! This is an excellent training course delivered at a unique location and close to the most wonderful time of the year. It also has LOTS of tutors per student! www.ccp4.ac.uk/schools/DLS-...
DLS/CCP4 Workshop 2025
www.ccp4.ac.uk
September 3, 2025 at 4:11 PM
Just a few days left to register for the next Diamond/CCP4 Data Collection and Structure Solution Workshop! This is an excellent training course delivered at a unique location and close to the most wonderful time of the year. It also has LOTS of tutors per student! www.ccp4.ac.uk/schools/DLS-...
Just a few days left to register for the next Diamond/CCP4 Data Collection and Structure Solution Workshop! This is an excellent training course delivered at a unique location and close to the most wonderful time of the year. It also has LOTS of tutors per student! www.ccp4.ac.uk/schools/DLS-...
DLS/CCP4 Workshop 2025
www.ccp4.ac.uk
September 3, 2025 at 4:11 PM
Just a few days left to register for the next Diamond/CCP4 Data Collection and Structure Solution Workshop! This is an excellent training course delivered at a unique location and close to the most wonderful time of the year. It also has LOTS of tutors per student! www.ccp4.ac.uk/schools/DLS-...
Reposted by Jon Agirre
Excited to share this story on the protein crystallography CURE I developed and have been teaching for the last 3 years!
www.vassar.edu/news/student...
This course is supported by my #CottrellScholars Award from RCSA.
@rescorp.org
@vassar.bsky.social
#grantsinaction #biochemistry
www.vassar.edu/news/student...
This course is supported by my #CottrellScholars Award from RCSA.
@rescorp.org
@vassar.bsky.social
#grantsinaction #biochemistry
July 31, 2025 at 2:15 PM
Excited to share this story on the protein crystallography CURE I developed and have been teaching for the last 3 years!
www.vassar.edu/news/student...
This course is supported by my #CottrellScholars Award from RCSA.
@rescorp.org
@vassar.bsky.social
#grantsinaction #biochemistry
www.vassar.edu/news/student...
This course is supported by my #CottrellScholars Award from RCSA.
@rescorp.org
@vassar.bsky.social
#grantsinaction #biochemistry
Reposted by Jon Agirre
We were pleased to publish some of the results from this course, some in our recent 'Empowering education through structural genomics' focused issue: journals.iucr.org/special_issu...
Excited to share this story on the protein crystallography CURE I developed and have been teaching for the last 3 years!
www.vassar.edu/news/student...
This course is supported by my #CottrellScholars Award from RCSA.
@rescorp.org
@vassar.bsky.social
#grantsinaction #biochemistry
www.vassar.edu/news/student...
This course is supported by my #CottrellScholars Award from RCSA.
@rescorp.org
@vassar.bsky.social
#grantsinaction #biochemistry
July 31, 2025 at 3:20 PM
We were pleased to publish some of the results from this course, some in our recent 'Empowering education through structural genomics' focused issue: journals.iucr.org/special_issu...
Reposted by Jon Agirre
Happy World Rain Day! It’s raining…
– Cats and dogs (English)
– Old ladies and sticks (Welsh)
– Like a pissing cow (French)
– As from Esteri’s ass (Finnish)
– Penguins headfirst (Uruguayan Spanish)
– Pilot whales (Faroese)
– Chair legs (Greek)
– Wheelbarrows (Czech)
– Men (hallelujah)
– Cats and dogs (English)
– Old ladies and sticks (Welsh)
– Like a pissing cow (French)
– As from Esteri’s ass (Finnish)
– Penguins headfirst (Uruguayan Spanish)
– Pilot whales (Faroese)
– Chair legs (Greek)
– Wheelbarrows (Czech)
– Men (hallelujah)
July 29, 2025 at 9:17 AM
Happy World Rain Day! It’s raining…
– Cats and dogs (English)
– Old ladies and sticks (Welsh)
– Like a pissing cow (French)
– As from Esteri’s ass (Finnish)
– Penguins headfirst (Uruguayan Spanish)
– Pilot whales (Faroese)
– Chair legs (Greek)
– Wheelbarrows (Czech)
– Men (hallelujah)
– Cats and dogs (English)
– Old ladies and sticks (Welsh)
– Like a pissing cow (French)
– As from Esteri’s ass (Finnish)
– Penguins headfirst (Uruguayan Spanish)
– Pilot whales (Faroese)
– Chair legs (Greek)
– Wheelbarrows (Czech)
– Men (hallelujah)
🏴🏴
July 27, 2025 at 8:07 PM
🏴🏴
AI chat bots behaving like science fiction AI chat bots because they were once trained on Asimov
In my latest (and last!) column for Science’s Expert Voices series, I write about the reasons behind AI chatbots’ “deceptive” behaviors (and why Claude threatened a fictional CEO with blackmail).
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Why AI chatbots lie to us
A few weeks ago, a colleague of mine needed to collect and format some data from a website, and he asked the latest version of Anthropic’s generative AI system, Claude, for help. Claude cheerfully agr...
www.science.org
July 25, 2025 at 10:49 PM
AI chat bots behaving like science fiction AI chat bots because they were once trained on Asimov
Reposted by Jon Agirre
Just realised that we've been doing Interviews With Authors on YouTube for a whole year!
I'd really appreciate receiving comments about these, e.g. suggest a structural biologist you would like us to interview
Here's a playlist with all the videos we've done so far: www.youtube.com/playlist?lis...
I'd really appreciate receiving comments about these, e.g. suggest a structural biologist you would like us to interview
Here's a playlist with all the videos we've done so far: www.youtube.com/playlist?lis...
Interviews with Authors - YouTube
www.youtube.com
July 18, 2025 at 9:37 AM
Just realised that we've been doing Interviews With Authors on YouTube for a whole year!
I'd really appreciate receiving comments about these, e.g. suggest a structural biologist you would like us to interview
Here's a playlist with all the videos we've done so far: www.youtube.com/playlist?lis...
I'd really appreciate receiving comments about these, e.g. suggest a structural biologist you would like us to interview
Here's a playlist with all the videos we've done so far: www.youtube.com/playlist?lis...
Reposted by Jon Agirre
Fascinating. Microsoft emailed me to say it was raising the price of Microsoft 365, but when i went to cancel it offered me me the old price — without all the AI bullshit.
It’s forcing AI on everyone and making them pay more for it, then only telling them they don’t have to if they try to cancel.
It’s forcing AI on everyone and making them pay more for it, then only telling them they don’t have to if they try to cancel.
July 19, 2025 at 3:11 AM
Fascinating. Microsoft emailed me to say it was raising the price of Microsoft 365, but when i went to cancel it offered me me the old price — without all the AI bullshit.
It’s forcing AI on everyone and making them pay more for it, then only telling them they don’t have to if they try to cancel.
It’s forcing AI on everyone and making them pay more for it, then only telling them they don’t have to if they try to cancel.
Reposted by Jon Agirre
Welcome to the new normal in Erurope
Please use mosquito repellent
Please use mosquito repellent
European nations report more local detections of chikungunya, dengue
Italy and France are now reporting local chikungunya cases, and 3 countries have confirmed local dengue infections.
www.cidrap.umn.edu/c...
Photo: UK College of Agriculture, Food & Environment/Flickr cc
Italy and France are now reporting local chikungunya cases, and 3 countries have confirmed local dengue infections.
www.cidrap.umn.edu/c...
Photo: UK College of Agriculture, Food & Environment/Flickr cc
July 19, 2025 at 6:48 AM
Welcome to the new normal in Erurope
Please use mosquito repellent
Please use mosquito repellent
Just realised that we've been doing Interviews With Authors on YouTube for a whole year!
I'd really appreciate receiving comments about these, e.g. suggest a structural biologist you would like us to interview
Here's a playlist with all the videos we've done so far: www.youtube.com/playlist?lis...
I'd really appreciate receiving comments about these, e.g. suggest a structural biologist you would like us to interview
Here's a playlist with all the videos we've done so far: www.youtube.com/playlist?lis...
Interviews with Authors - YouTube
www.youtube.com
July 18, 2025 at 9:37 AM
Just realised that we've been doing Interviews With Authors on YouTube for a whole year!
I'd really appreciate receiving comments about these, e.g. suggest a structural biologist you would like us to interview
Here's a playlist with all the videos we've done so far: www.youtube.com/playlist?lis...
I'd really appreciate receiving comments about these, e.g. suggest a structural biologist you would like us to interview
Here's a playlist with all the videos we've done so far: www.youtube.com/playlist?lis...
Structural variation in positive subsites in loop regions demonstrating high structural variability suggests potential differences in substrate specificity in family 168 glycoside hydrolases #GlycosideHydrolases #Fucoidanases #MarineBacteria doi.org/10.1107/S205...
July 17, 2025 at 3:30 PM
As the community gets ready for #ACA2025, we're proud to present this interview with @gabbygrowsxtals.bsky.social Vivian Stojanoff and @xtalmaker.bsky.social on how to prepare for successful protein crystallisation experiments! 🥳🥳 youtu.be/m34RI500OFU?...
Preparing for successful protein crystallization experiments
YouTube video by International Union of Crystallography
youtu.be
July 14, 2025 at 9:02 AM
As the community gets ready for #ACA2025, we're proud to present this interview with @gabbygrowsxtals.bsky.social Vivian Stojanoff and @xtalmaker.bsky.social on how to prepare for successful protein crystallisation experiments! 🥳🥳 youtu.be/m34RI500OFU?...
Reposted by Jon Agirre
Excited that our article made the cover of the July issue of @actacrystf.iucr.org!
Congrats to my coauthors @gabbygrowsxtals.bsky.social & Vivian Stojanoff!
Grateful for #NIH NIGMS R24 National Resource grant that enables workshops like the 2023 SAMPREP workshop @ @acastructuralsci.bsky.social
Congrats to my coauthors @gabbygrowsxtals.bsky.social & Vivian Stojanoff!
Grateful for #NIH NIGMS R24 National Resource grant that enables workshops like the 2023 SAMPREP workshop @ @acastructuralsci.bsky.social
The July issue is out! tinyurl.com/y25fxe86
The cover shows a rainbow of protein crystals taken from a Topical Review on 'Preparing for successful protein crystallization experiments'. Take a look at doi.org/10.1107/S205...
The cover shows a rainbow of protein crystals taken from a Topical Review on 'Preparing for successful protein crystallization experiments'. Take a look at doi.org/10.1107/S205...
July 3, 2025 at 7:18 PM
Excited that our article made the cover of the July issue of @actacrystf.iucr.org!
Congrats to my coauthors @gabbygrowsxtals.bsky.social & Vivian Stojanoff!
Grateful for #NIH NIGMS R24 National Resource grant that enables workshops like the 2023 SAMPREP workshop @ @acastructuralsci.bsky.social
Congrats to my coauthors @gabbygrowsxtals.bsky.social & Vivian Stojanoff!
Grateful for #NIH NIGMS R24 National Resource grant that enables workshops like the 2023 SAMPREP workshop @ @acastructuralsci.bsky.social
Reposted by Jon Agirre
🚨We've updated our preprint "Frustration, Dynamics, and Catalysis" ✨ We appreciate RT ☺️
A short 🧵1/8: We expanded the conceptual connection between the energy landscapes theory and catalysis, added new figures, and clarified how local frustration shapes enzyme function.
arxiv.org/pdf/2505.00600
A short 🧵1/8: We expanded the conceptual connection between the energy landscapes theory and catalysis, added new figures, and clarified how local frustration shapes enzyme function.
arxiv.org/pdf/2505.00600
July 9, 2025 at 9:17 AM
🚨We've updated our preprint "Frustration, Dynamics, and Catalysis" ✨ We appreciate RT ☺️
A short 🧵1/8: We expanded the conceptual connection between the energy landscapes theory and catalysis, added new figures, and clarified how local frustration shapes enzyme function.
arxiv.org/pdf/2505.00600
A short 🧵1/8: We expanded the conceptual connection between the energy landscapes theory and catalysis, added new figures, and clarified how local frustration shapes enzyme function.
arxiv.org/pdf/2505.00600
We’ve got some more ECR interviews coming — watch this space!
Together with Toyin Asojo, Graham Chakafana and Craig Smith, we have recently edited a focused issue on 'Empowering education through structural genomics', featuring the work of both undergrads and high school students – watch Toyin interview Aruesha, Aryana & Raymond www.youtube.com/watch?v=KJkN...
Structures of Trichomonas vaginalis macrophage migratory inhibitory factor
YouTube video by International Union of Crystallography
www.youtube.com
July 8, 2025 at 9:20 AM
We’ve got some more ECR interviews coming — watch this space!
Reposted by Jon Agirre
More arguments for choosing society journals, where any profits are ploughed back into science! For structural biology, please consider @actacrystd.iucr.org, @actacrystf.iucr.org and @iucrj.iucr.org!
Where is the money going? In the case of for-profit publishers it's very clear:
Your open access fees fund corporate profit margins.
Profit margins for large academic publishers can far exceed those of household names like Amazon and Apple.
chart source: bit.ly/4leULKi
#scipub #academicsky
Your open access fees fund corporate profit margins.
Profit margins for large academic publishers can far exceed those of household names like Amazon and Apple.
chart source: bit.ly/4leULKi
#scipub #academicsky
July 8, 2025 at 7:05 AM
More arguments for choosing society journals, where any profits are ploughed back into science! For structural biology, please consider @actacrystd.iucr.org, @actacrystf.iucr.org and @iucrj.iucr.org!
Reposted by Jon Agirre
Together with Toyin Asojo, Graham Chakafana and Craig Smith, we have recently edited a focused issue on 'Empowering education through structural genomics', featuring the work of both undergrads and high school students – watch Toyin interview Aruesha, Aryana & Raymond www.youtube.com/watch?v=KJkN...
Structures of Trichomonas vaginalis macrophage migratory inhibitory factor
YouTube video by International Union of Crystallography
www.youtube.com
July 6, 2025 at 9:52 AM
Together with Toyin Asojo, Graham Chakafana and Craig Smith, we have recently edited a focused issue on 'Empowering education through structural genomics', featuring the work of both undergrads and high school students – watch Toyin interview Aruesha, Aryana & Raymond www.youtube.com/watch?v=KJkN...
Together with Toyin Asojo, Graham Chakafana and Craig Smith, we have recently edited a focused issue on 'Empowering education through structural genomics', featuring the work of both undergrads and high school students – watch Toyin interview Aruesha, Aryana & Raymond www.youtube.com/watch?v=KJkN...
Structures of Trichomonas vaginalis macrophage migratory inhibitory factor
YouTube video by International Union of Crystallography
www.youtube.com
July 6, 2025 at 9:52 AM
Together with Toyin Asojo, Graham Chakafana and Craig Smith, we have recently edited a focused issue on 'Empowering education through structural genomics', featuring the work of both undergrads and high school students – watch Toyin interview Aruesha, Aryana & Raymond www.youtube.com/watch?v=KJkN...