New on the CryoET Data Portal: ~27,000 tomograms of affinity-captured lysosomes from HEK293T cells across 4 physiological states. Includes raw data, AreTomo3 reconstructions & Membrain-Seg annotations. Openly available for reuse!

cryoetdataportal.czscience.com/depositions/...

#TeamTomo if you want to use CTF-corrected 3D subtomos from AreTomo3 in RELION v.5.1 you can use this updated script:

github.com/Phaips/aretomo3torelion5

Check out 'the website' by Phil&Flo - a tomo processing pipeline/tutorial from frame to structure. For easy implementation of the Aretomo3 to RELION5 pipeline, or your students first dataset, get processing!

Great guide, and very comprehensive! Also the scripts you wrote for converting aretomo3 to relion are so useful 😄

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!
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New Title Alert: AreTomo3- a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.

More here: https://github.com/czimaginginstitute/AreTomo3

#SBGrid #structuralbiology #SBGridsoftware

Like cryo-CARE and DDW, Icecream🍧is a post-processing tool that requires ODD/EVEN tomograms generated from the split of raw movie frames, which are now super easy to obtain e.g. from IMOD alignframes or AreTomo3.

Warptools has an inbuilt aretomo3 wrapper that you can use. If your plan is to use M, i recommend preprocessing the data with warptools. Pytom-match pick natively supports warptools xml files for on the fly filter calculation.

New Title Alert: AreTomo3- a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.

More here: https://github.com/czimaginginstitute/AreTomo3

#SBGridSoftware #SBGrid #structuralbiology

Does anybody have a working protocol for a pipeline including aretomo3 to pytom-tm to warptools for #STA? I would ideally like to use M for the final refinements instead of being confined to relion5. Any suggestions/resources would be welcome! #teamtomo #cryoet #cryoem

Yes, at least with respect to motion correction. I *think* having very short duration frames may still improve CTF estimation. For MotionCor3 and AreTomo3 the 'frame integration file' option may be convenient for you here, it's described in the AreTomo3 manual PDF

Technical Notes: April's software push includes updates to AlphaPulldown, AreTomo3, Chai-1, Fpocket, IDPConformerGenerator, IMOD, JupyterLab, pdb_extract, PEET, PROPKA, RDKit, RECOVAR, relion_composite_masks, Tardis, Warp, and XDS.

More here: buff.ly/iJG4j6G

#SBGrid #Software

Technical Notes: March's software push includes updates to 3D Slicer, AreTomo3, ATSAS, BindCraft, ChimeraX, Doppio, DAQ Score, EMAN2, Geneious, Hole, MDAnalysis, VMD, and Warp.

More here: buff.ly/McsvSl9

#SBGrid #Software