Using the amazing #pytom-match-pick we guide you through particle picking. From the template matching results we show you how to perform STA in #RELION5 pushing Ribosomes to their absolute limit (Nyquist)!
3 /🧵
We decided to summarize our (the @cellarchlab.com group) most common workflows! The Tutorial guides you through tomogram pre- and postprocessing using either #RELION5, #Scipion, or #AreTomo3. With the Chlamy dataset (www.ebi.ac.uk/empiar/EMPIA...) as a possible resource for all those steps!
2/🧵
Finally got some time to properly test #RELION5 complete pipeline, starting from raw frames to STA. 22 tilt-series (from EMPIAR-11830), picking done with pytom, 14600 final particles, FSC 4.1-ish on the LSU (Nyquist bin1 3.8). Ofc it's a ribosome 😅 but now I can try with smthng more chlengin
#CryoET
To get a high-resolution reconstruction, we tried a lot of things, but the map quality was never all that great. Until #RELION5 #Blush came along and provided us with an isotropic map into which we were able to properly refine a model that also agreed with AlphaFold predictions.
We're pleased to announce that #RELION5 is now available for beta testing! 🥳🥳🥳 Download it for free from github.com/3dem/relion/...
#OpenSoftwareAcceleratesScience
This was the last preprint before our #RELION5 beta release, which I will hopefully get to by tomorrow afternoon or on Thursday. #staytuned
Now on @biorxivpreprint.bsky.social: Dari Kimanius' paper on #Blush regularisation, a machine-learning based prior in #RELION5 trained on EMDB #cryoEM half-maps, which he uses to solve a #cryoEM data set of a 40 kDa protein:RNA complex that was previously intractable!
www.biorxiv.org/content/10.1...
The #OpenSoftwareAcceleratesScience code can already be downloaded from the link below. However, it may be worth waiting another week or so, when we release #RELION5 for easier installation and full integration in its GUI.
Blush is a denoising neural network that is trained on many EMDB #cryoEM half-maps using a noise2noise framework. It replaces the Fourier-based (smoothness) prior inside the iterative RELION refinement. That @biorxivpreprint.bsky.social will be next, as also Blush will be part of #RELION5.
Next up in our preparation for #RELION5 will be a
@biorxivpreprint.bsky.social to describe #DynaMight: our solution for ’exploring protein *Dyna*mics that *Might* improve your map’ by the amazing Johannes Schwab. #staytuned #cryoEM
