Liya Mukhamedova

socially awkward introvert/structural biologist

[Liya Mukhamedova @LMumrik]

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

[Liya Mukhamedova @LMumrik]

Теперь тьма окончательно абсолютна.

[Liya Mukhamedova @LMumrik]

@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 :(

[Liya Mukhamedova @LMumrik]

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)

[Liya Mukhamedova @LMumrik]

Are those pre-Christmas bells in our sample? 🤔

[Liya Mukhamedova @LMumrik]

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

[Liya Mukhamedova @LMumrik]

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)

[Liya Mukhamedova @LMumrik]

@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.

[Liya Mukhamedova @LMumrik]

@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?

[Liya Mukhamedova @LMumrik]

@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 :)

[Liya Mukhamedova @LMumrik]

@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" :)

[Liya Mukhamedova @LMumrik]

@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?

[Liya Mukhamedova @LMumrik]

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

[Plevka Lab @PlevkaLab]

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

[Liya Mukhamedova @LMumrik]

@sonjawelsch Pareidolia as it is :)

[Liya Mukhamedova @LMumrik]

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

[Tomas Malinauskas @t_malinauskas]

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

[Liya Mukhamedova @LMumrik]

@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 🙂

[Liya Mukhamedova @LMumrik]

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 🙃 )

[Liya Mukhamedova @LMumrik]

@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