We solved a high resolution structure of the nucleosome core particle directly from nuclear extract from a single T25 flask (3 mL culture). No affinity purification. No sucrose gradients. Just lysate on grids. Raw data available now for anyone who wants to reprocess. www.biorxiv.org/content/10.6...

I am very proud to my student Stasia whose manuscript about the nucleocapsid assembly of an ephemerovirus is now available to read. Within three years she managed to defend her thesis, submit the manuscript and secure a postdoc job, while adapting to the UK weather! www.biorxiv.org/content/10.6...

A little summary of some events. Version 1.

@joachimgoedhart.bsky.social & #microscopy friends, we're using ymScarlet-i3. It's the best general purpose red FP we've tried in budding yeast. But in our hands it photobleaches really fast when exposed relatively low-intensity *488 nm* laser light (~20 W/cm^2). Have you seen this? Thoughts?

Better and faster microscope generates large amount of data which then lead to high resolution image. With AI server hunger for more data storage too, look like data storage will be next bottleneck in image processing. Still this is pale in comparison with data generated by LHC per day.

This ‘landmark’ study describes the structural mechanism of strand exchange by the RAD51 filament using cryogenic structural, biochemical, and single-molecule analyses. buff.ly/Ieh84gj

Over five years of work has gone into our new preprint! The #cryoEM structure of a human RAD51 filament caught at the point of strand exchange 🧬 www.biorxiv.org/content/10.1...

TIL, New Zealand allows direct prescription drug advertising to consumer.

Join the first Keystone conference dedicated to DNA replication gaps and cancer! Send an abstract to be selected for a talk. www.keystonesymposia.org/conferences/...

Just only discover the "--reuse_scratch" and "--keep_scratch" option in RELION, to minimize repetitively copying the same particle set into the cache directory for each job. I should have read more carefully at the long list of command options available.

Mastering the act to remotely wake up a workplace Linux machine from sleep using a smartphone at home with a single click. By putting PC to sleep, is estimated to reduce the machine's power consumption by ten times when compared to its idle power consumption.

Source code available; easy to install; run test dataset without error; and job finish in less than a minute. 🤯 But it using a non-standard input and output format which require installation of additional software 😫

cryoSPARC benchmark of some GPU workstation in the department

mamba is faster than conda 🐍

Spent 1 hours trying to install a software, spent another 3 hours trying to work out how to use the software (poor documentation), only for the job to quit with an error: CUDA out of memory. 🥲

So it is possible to finish the RELION 2D classification with EM after VDAM using additional argument "--grad_em_iters 25"

Most cryoEM lab workstation: AMD ThreadRipper + 4090 Me: Ryzen 9 + 4070 Ti Super

Human Primosome (Initiation state) doi.org/10.1111/febs... #MolecularNode

Interesting, (1xMPI, 64 Threads, --cpu) RELION's VDAM rans faster than (1xMPI, 32 Threads, 1 GPU, --gpu) RELION's VDAM in our HPC. Also execute RELION's VRAM command with either mpirun or mpiexec are significant slower than srun command.

From Blue Letter F to Blue Birds, now to Blue Sky.