Liya Mukhamedova

@MojeMenoJeNikto How about "The structure of XXX", or anything else that is remarkable about the structure of XXX?

#CryoEM community, when you used a combination of SPA and ET to get your results, what would you use in the manuscript title? "Cryo-electron microscopy of XXX" or "Cryo-electron tomography of XXX", or something else? Want to preserve the method in the title

Теперь тьма окончательно абсолютна.

@DsSvetlov @GrigoryTag Honestly, I freaked out when I saw a guy in uniform at the preview as a response to my post 😅 Thanks a lot for the suggestion! Unfortunately, US is a bit too far for my current family situation :(

So, well, here is a human being with almost 10 years of experience in Structural Virology with apparently wrong passport to be born with, searching for a job in a field somewhere in EU. The human even has a residency permit in Cz. Any ideas? (Please)

Are those pre-Christmas bells in our sample? 🤔

@parameciumbrain @OrsDragonfly3D OMG, yes, I can imagine how confusing it all sounds :D Anyways, thanks a lot for helping with the issue!

@LMumrik @OrsDragonfly3D Interesting! I'm terrible at picturing things in my head so I'm sure we'll be able to solve it over zoom =)

So, @OrsDragonfly3D users, I have a question. How to make Multi-ROI active for the training? Don't tell me, I segmented a day out of my life for nothing 😅 (Sharing is carrying: if u don't know the answer, pls share the question)

@parameciumbrain @OrsDragonfly3D Yes, I picked the slices and pained them again, then tried: 1) open all as it is freshly painted, 2) resample freshly painted multiROI to original tomo and open. In both cases, I was able to pick a tomogram for training, but not a multiROI, neither a mask.

@LMumrik @OrsDragonfly3D If you want to just train on select slices, you can create a new ROI (not attached to the multiroi) and paint all of the marked slices. Then input that ROI in the mask option of deep learning tool.

@parameciumbrain @OrsDragonfly3D Update: I redone the imput only with selected slices, and now I can resample multiROI to original tomo. But I guess, if I want to train it on selected slices, I better not. As well, what came to my mind, can't mrc format of the tomo be a problem here, actually?

@LMumrik @OrsDragonfly3D If you have time later tonight (in like 4 hours) I could hop on a zoom call and see if we can figure it out.

@parameciumbrain @OrsDragonfly3D Wow! Thanks a lot, I'll try to sustain. Anyway, I wanted to start from the start using the selected slices and see if that will work. So I there is a huge possibility I will be up :)

@parameciumbrain @OrsDragonfly3D I used the whole tomo, and I tried to rewrite the geometry using this exact tomo. The selected slices were just a trial, aka "may be this will work, ah, nope, nevermind" :)

@LMumrik @OrsDragonfly3D Hmm, I see your input is marked slices, did you make the multiROI using the full volume or just using the market slices?

@parameciumbrain @OrsDragonfly3D Hello, thanks a lot for your advice! Tried to resample, but it doesn't seem to be possible. Somehow, it doesn't allow me to choose the geometry of my tomo 🤷‍♀️ It feels like tomo and segmentation somehow exist separately (if this even possible). May be I did it wrong?

@LMumrik @OrsDragonfly3D Is it the right geometry? Right click the multiRoi in the data properties list and try resampling the geometry to your image.

Nowadays everyone can come close to Nyquist, but how far can you go? 🤔

A few of us are representing the lab at the 6th Austrian #cryoEM symposium at #IMP in Vienna 🇦🇹 Check out posters nr. 10, 13, 14, 18 and 41 if you want to find out what we do 😎 Fig. 1: ordered conformation Fig. 2: disordered conformation

@sonjawelsch Pareidolia as it is :)

@LMumrik thingswithfaces.com

I think our loading station goes through some sort of existential crisis

X-ray crystallography, AlphaFold, and cryo-EM.

@SchejbalJLab I don't want to spoil the possible paper or Twitter thread called "An importance of a control sample", but yes, we are trying to identify the viral proteins 🙂

@LMumrik I forgot you are doing whole viruses on a cell surfaces. Then it will need to be processed. Purified proteins would be easier. Ask the core about low-input sample processing protocols, they should have some. What are you hoping to see in MS? The viral proteins?

Yet another attempt to ask the Twitter cryoEM community (never really worked but may be this time). Did any of you tried to do the Masspec from the cryoEM grid? If so, I would be happy to have a protocol for a sample prep 😊 (repost gives + points to good carma 🙃 )

@SchejbalJLab Thank you!I'll consult our MS facility about that.There is one complication, and it is that the sample is not homogeneous:it is practically bunch of infected cells.I have very limited experience with MS,so it is hard for me to imagine if DESI will be good choice in this situation

@LMumrik OK, haven't tried it myself but have you looked into DESI, MALDESI and related ablation/desorption MS techniques? These should be able to work with the grid directly without any need for further sample prep. The choice will be most likely guided by the mass of the analyte.