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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...

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.

Hard drives on backorder for two years as AI data centers trigger HDD shortage — delays forcing rapid transition to QLC SSDsThe AI boom might help QLC overtake TLC in the next two years.www.tomshardware.com

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

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 😫

Graphormer/distributional_graphormer/protein at dig-v1.0 · microsoft/GraphormerGraphormer is a general-purpose deep learning backbone for molecular modeling. - microsoft/Graphormergithub.com

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.