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Guillaume GaullierFinally, one thing that struck me is how friendly this conference and community are!I sometimes write to the CCPEM mailing list and CryoSPARC forum, and generally try to answer questions when I can contribute something helpful. A few people told me they recognized my name from there and had appreciated something I posted. One person even told me they had been hoping we'd meet in person at the conference. This was incredibly nice to hear!I hope I'll be able to attend next year.<a href="https://fediscience.org/tags/CCPEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CCPEM</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

Guillaume GaullierOne highlight from Friday that I forgot: Alister Burt's talk on his efforts to build <a href="https://fediscience.org/tags/TeamTomo" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#TeamTomo</a>, a set of community-supported software packages and metadata standards for <a href="https://fediscience.org/tags/cryoET" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoET</a>. This is difficult work, and less rewarding for those in academia, but so essential. It's great to see progress on this front.The other great news from Alister's talk: Warp is now supported on Linux!Finally, I'll remember his advice "think about geometry, and use it if you can" when assigning initial particle orientations for subtomogram averaging.<a href="https://fediscience.org/tags/CCPEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CCPEM</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

Guillaume GaullierAnd some highlights from earlier today:CryoCloud.io seems like a great single-particle analysis suite. They developed their own deep learning particle picker, which apparently outperforms Topaz. I hope this will be published, very curious to see how it works. It’s always great to have more options for particle picking (the most difficult and critical step of SPA in my opinion). They also developed a metric to quantify resolution anisotropy without requiring particle poses (which are not part of the mandatory items for deposition, therefore rarely available).Alexander Shtyrov from Garib Murshudov’s group showed very interesting results about learning atomic electron scattering factors from high-resolution cryoEM maps. This will hopefully help us use these maps to their full potential (pun intended) when doing atomic model building and refinement. The ideal training set for these methods are zero-dose extrapolated maps, which are still a rarity (there might be only one deposited to date? from Chris Russo’s HexAuFoil paper).<a href="https://fediscience.org/tags/CCPEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CCPEM</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

Guillaume GaullierThese three days have passed by so fast, and here I am collecting my thoughts already on the way back home…More highlights from Thursday:Jessie Zhang showed great progress with the development of the Laser Phase Plate! Data collection with LPP on is now routine for both single-particle and tomography. It is still unclear whether fully in-focus imaging is possible; if so, it will of course change how we do CTF estimation, but the rest might work just the same? Unclear until they try it.Jude Short in Chris Russo’s group has a working implementation of zero-dose extrapolation, presumably more user-friendly than the scripts that came with the HexAuFoil paper.Hannah Bridges from StructuraBio (makers of CryoSPARC) reprocessed my dataset EMPIAR-10739 and got vastly improved results. This was so cool to see! Looking forward to seeing this case study in the CryoSPARC guide.<a href="https://fediscience.org/tags/CCPEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CCPEM</a> <a href="https://fediscience.org/tags/cryoem" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoem</a>

Guillaume GaullierCouple of highlights from today Thursday (well, technically yesterday now, since it's getting late).LocScale version 2 from Arjen Jakobi's group seems very helpful and I will try it as soon as I am back at the lab.Doppio seems super nice, and has been made easier to install. I also need to try it. It would be nice to have an alternative to CryoSPARC, with a nicer workflow visualization than stand-alone RELION. Not sure what are the pros/cons between Doppio and Scipion, since they seem to do similar things. I need to read up about this.RECOVAR from Amit Singer's group seems like a good tool to analyze heterogeneity. Main take-away from the talk: enough noise in the particle images can make most such programs "hallucinate" heterogeneity, so one must be very careful when interpreting results!<a href="https://fediscience.org/tags/CCPEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CCPEM</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

Guillaume GaullierA first highlight: Stephen Muench's talk yesterday about rapid vitrification.I had read some papers from his group before, and enjoyed them a lot. The talk was excellent, and there are some great things brewing. Set a PubMed alert if you are interested in rapid vitrification.My take-aways:- We cannot outrun particles colliding with the air-water interface (brownian motion in a thin film is simply too fast). - But vitrifying fast is still very helpful in many cases. - Revisiting conventional blotting and plunge-freezing still has potential. See <a href="https://cryopreparation.com" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://cryopreparation.com</a><a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

Guillaume GaullierAt the <a href="https://fediscience.org/tags/CCPEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CCPEM</a> Spring Symposium since yesterday, and it's been so nice! ❄️ 🔬The schedule is packed and I try to pay attention to the talks, so no live posting. But I'll try to post some of my personal highlights under this post as I find time to reflect. 🧵Schedule: <a href="https://www.ccpem.ac.uk/symposium/spring-symposium-2025/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.ccpem.ac.uk/symposium/spring-symposium-2025/</a><a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

PLOS BiologyA precursor procapsid is initially formed during <a href="https://fediscience.org/tags/bacteriophage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bacteriophage</a> assembly, but how? The <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> structure of the scaffolding protein complex & portal within <a href="https://fediscience.org/tags/phage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#phage</a> P22 procapsid reveals how this complex orchestrates the initiation of procapsid assembly <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@PLOSBiology</a> <a href="https://plos.io/44B71iE" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://plos.io/44B71iE</a>

Guillaume GaullierLooking for a <a href="https://fediscience.org/tags/postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#postdoc</a> position?Come work with us on CO2 fixation in <a href="https://fediscience.org/tags/cyanobacteria" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cyanobacteria</a> using <a href="https://fediscience.org/tags/biochemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biochemistry</a> and <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>! 🦠 🧪 🧫 ❄️🔬We are a friendly group. 🙂 <a href="https://www.blikstadlab.org/open-positions.html" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.blikstadlab.org/open-positions.html</a><a href="https://fediscience.org/tags/job" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#job</a> <a href="https://fediscience.org/tags/postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#postdoc</a>

PLOS BiologyReports of diverse stoichiometries have complicated our understanding of the complex between ALK kinase and its <a href="https://fediscience.org/tags/cytokine" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cytokine</a> ligand ALKAL2. <a href="https://mstdn.science/@janfelix" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@janfelix</a> &co reanalyze <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> data to clarify the situation <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@PLOSBiology</a> <a href="https://plos.io/4lvRfvu" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://plos.io/4lvRfvu</a>

PLOS BiologyBacterial ABC peptide transporters are involved in processes like nutrient uptake. This study solves <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> structures of the <a href="https://fediscience.org/tags/Ecoli" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Ecoli</a> dipeptide <a href="https://fediscience.org/tags/transporter" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#transporter</a> DppABCDF in both apo & ATP analog-bound forms, providing insights into assembly & import mechanism <a href="https://fediscience.org/tags/plosbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#plosbiology</a> <a href="https://plos.io/3DxP8pU" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://plos.io/3DxP8pU</a>

Guillaume GaullierNew preprint I contributed to: <a href="https://doi.org/10.1101/2025.02.17.638584" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1101/2025.02.17.638584</a>I helped this group do atomic model building and refinement in their <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> maps.This was more model building than I had done with all my previous projects combined! And it made me streamline the process I described in this thread: <a href="https://fediscience.org/@Guillawme/113281867808537736" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://fediscience.org/@Guillawme/113281867808537736</a>

StructBiolCommunicationsCryoCrane, a visualization tool for cryo-EM screening data, aims to provide an intuitive way to visualize micrographs and to speed up data analysis. <a href="https://mstdn.science/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> <a href="https://mstdn.science/tags/SampleOptimization" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SampleOptimization</a> <a href="https://mstdn.science/tags/GridScreening" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GridScreening</a> <a href="https://doi.org/10.1107/S2053230X25000081" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1107/S2053230X25000081</a>

Guillaume GaullierThe micrograph denoiser in CryoSPARC is really good! Fast training and denoising, excellent output (more helpful than topaz denoise; both run with their default settings).Why didn't I start using it earlier??<a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

eLifeCryogenic Electron Microscopy: MagIC beads for scarce macromolecules. <a href="https://fediscience.org/tags/CryoEm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEm</a> <a href="https://elifesciences.org/articles/105335?utm_source=mastodon&utm_medium=social&utm_campaign=organic_insights" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://elifesciences.org/articles/105335?utm_source=mastodon&utm_medium=social&utm_campaign=organic_insights</a>

Guillaume GaullierIt's great to *finally* have both a direct work-related reason and enough free time these past two days to immerse myself in the two atomic resolution <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> papers from 2020 and give them a good, thorough, cover-to-cover read. 📖 🤓 ❄️ 🔬Feeling like it's an important step through the never-ending backlog of important papers in this field. 😌Nakane et al. 2020: <a href="https://doi.org/10.1038/s41586-020-2829-0" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1038/s41586-020-2829-0</a>Yip et al. 2020: <a href="https://doi.org/10.1038/s41586-020-2833-4" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1038/s41586-020-2833-4</a>

StructBiolCommunicationsCryoCrane is a visualization tool for cryo-EM screening data that aims to provide an intuitive way to visualize micrographs and to speed up data analysis. <a href="https://mstdn.science/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> <a href="https://mstdn.science/tags/SampleOptimization" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SampleOptimization</a> <a href="https://mstdn.science/tags/GridScreening" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GridScreening</a> <a href="https://doi.org/10.1107/S2053230X25000081" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1107/S2053230X25000081</a>

Stephen RoyleThis is pretty amazing. TMEM206 structure determined using a single HEK cell colony!"MISO: Microfluidic protein isolation enables single particle cryo-EM structure determination from a single cell colony”<a href="https://www.biorxiv.org/content/10.1101/2025.01.10.632437v1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2025.01.10.632437v1</a><a href="https://biologists.social/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://biologists.social/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

Dave nλ=2dsinθNEW - From us!Capture, mutual inhibition and release mechanism for aPKC–Par6 and its multisite polarity substrate Lgl <a href="https://www.nature.com/articles/s41594-024-01425-0" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.nature.com/articles/s41594-024-01425-0</a>It's be a long and difficult birth, but it is finally out there. Lovely bit of integrative CryoEM revealing a crucial kinase/substrate complex in the determination of cell polarity - how cells know which way is up. <a href="https://xtaldave.net/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://xtaldave.net/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> <a href="https://xtaldave.net/tags/MX" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MX</a> <a href="https://xtaldave.net/tags/Crystallography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Crystallography</a> <a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a>

Dave nλ=2dsinθStructural mechanism of CB1R binding to peripheral and biased inverse agonists | Nature CommunicationsLovely bit of work. <a href="https://xtaldave.net/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> <a href="https://xtaldave.net/tags/Crystallography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Crystallography</a> <a href="https://xtaldave.net/tags/Science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Science</a> <a href="https://xtaldave.net/tags/Research" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Research</a> <a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a> <a href="https://www.nature.com/articles/s41467-024-54206-0" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.nature.com/articles/s41467-024-54206-0</a>

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