Muyuan Chen is one of (maybe the?) primary developer of the sub-tomogram averaging portion of the EMAN2 software package (linked below in another comment). Typically what you do is take a 3D tomogram (think like a scan) using a microscope, but it's extremely noisy. Then you go through and extract all the particles that are identical, but in different orientations, in the tomogram. So if the same protein is there multiple times, you can align them to each other, and average them together to increase the signal. Then you clone back in the higher signal averaged volume at the position and orientation that you found them in originally.<p>The one-line command to go from EMAN2 coordinates to Unreal Engine 5 is kind of crazy.<p>As usual on these (rare) threads, I'm happy to answer any questions about structural biology or cryo-EM.
This reminds me of the amazing molecular animations of Drew Berry, which he showed in this TED talk:<p><a href="https://youtu.be/WFCvkkDSfIU?si=JNe06VS8TjIrHpqh" rel="nofollow">https://youtu.be/WFCvkkDSfIU?si=JNe06VS8TjIrHpqh</a><p>Which was 12 years ago! After watching that video, I had a much greater appreciation for how our bodies are made up of trillions of tiny protein machines. Fascinating stuff!!
One of videos:<p><a href="https://twitter.com/manorlaboratory/status/1763094135639294366/video/4" rel="nofollow">https://twitter.com/manorlaboratory/status/17630941356392943...</a><p>Anybody came across the code?
Reminds me of the drawings of David Goodsell:<p><a href="https://ccsb.scripps.edu/goodsell/" rel="nofollow">https://ccsb.scripps.edu/goodsell/</a><p>which are similarly about the 'packed' nature of cells.
If you get a kick out of 3D renderings of cells and molecules, you're gonna have a field day with the work done at <a href="https://random42.com/" rel="nofollow">https://random42.com/</a>. PSA: I started working there as a 3D artist but now lead the interactive department. You'd be surprised at how much a good art direction really makes a difference in scientific visualization. Real-time graphics advanced considerably in the last couple years but it's always a challenge to transport that nice, smooth pre-rendered look over to mobile devices and the web at 60 frames per second (90 on virtual reality headsets, to boot...)
this reminds me of the video from years ago that blew my mind:<p><a href="https://vimeo.com/76306502" rel="nofollow">https://vimeo.com/76306502</a>
I would like to ask a question and add before that that I have no intent to judge, discredit or diminish the value of this. It’s merely that I really don’t understand and would like to gain insight.<p>The question is: How is this a scientific contribution?<p>Or, to ask it differently: What makes this a scientific contribution?
This is fascinating to watch.<p>I understand that they get the proteins from PDB/ChimeraX, but how much manual process is involved to map and place the individual proteins? The paper says it gets the protein locations from CryoET tomograms, but I'd be surprised if these let you automatically identify which proteins are where, and exactly how to place them, and even less so how the ligomers bind together to form larger structures - for example, in the video the membrane surfaces are very smooth, and look almost textbook picture perfect, which suggests they come from a hardcoded model or are smoothed in some way. One part of the paper mentions subatomic averaging from the tomogram, but another mentions:<p>> From a tomogram (Figure3a), we select the particles and determine the orientation of the crown of the spike, as well as the stalk that connects the spike to the membrane<p>Is this a manual process, where the researcher is using his mental model of how the proteins are fit and placing/rotating individual proteins? Or do the tools they developed let this be automated. Both are impressive! If the former, I'm blown away by the effort it must take to make these kinds of videos.
People overlook game engines for plotting and data visualization.<p>You can have your character fly around whatever math/geometry you plotted. It’s great.