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Cryo EM Tutorials
เข้าร่วมเมื่อ 14 เม.ย. 2020
This is a channel devoted to tutorials on the use of cryo EM and structural biology softwares.
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Localized Refinement in cryoSPARC (NSP15 Case Study)
มุมมอง 7K3 ปีที่แล้ว
This is a link to the paper discussed: www.nature.com/articles/s41467-020-20608-z
Localized mask Creation with Chimera (Segger)
มุมมอง 8K3 ปีที่แล้ว
This is the method I used in the following paper: www.nature.com/articles/s41467-020-20608-z
Picking Holes For Collection in Serial EM
มุมมอง 5803 ปีที่แล้ว
Picking Holes For Collection in Serial EM
Slecting Grid Squares for Collection in Serial EM
มุมมอง 8423 ปีที่แล้ว
Slecting Grid Squares for Collection in Serial EM
Preparing a Reference Image in Serial EM
มุมมอง 5203 ปีที่แล้ว
Preparing a Reference Image in Serial EM
Laplachain Picking (Auto Picking) in RELION
มุมมอง 2.7K4 ปีที่แล้ว
Laplachain Picking (Auto Picking) in RELION
you did not explian the symmetry expansion and the final step where how to merge all the data after the individual refinment
Waiting for the rest of the sessions 🙏
thanks
How can I understand which particle I should select, if my micrograph is not showing particel like you. if I have thousands of micrograph, at least how many micrograph I should use for manual picking, If my particel size is 20A,
Hi, thanks a lot for this tutorial. I have a question, Did you make some video about 3D classification?
Hi, do you have the step-by-step turorial or case study for local refinement in cryoSparc v4.2.1? Thank you.
I have a local refinement tutorial in this channel. The only change from that video, is you no longer need to measure the center of your mask manually. Cryosparc now does that automatically in v4.2.
@@cryoemtutorials5598 Thanks so much! I am a postdoc from HMS ^_^
🎉
Would you please create a video of Bayesian polishing of particles imported from cryosparc using csparc2star program.!
Does it work on small proteins like 60kD or it’s good for big proteins only ??
Localized refinement just ignores signal from outside of your mask when it is aligning your particle images. As the size of your particle decreases, there is less and less signal contributed from each image to the final map. So it is still worth trying on any protein, but the benefit of localized refinement for something small will likely not be as noticeable as the resolution increase for a large protein. If you are working with a small protein, I would say that the biggest increase in resolution outside of having more particles, would be a more homogeneous data set. Try optimizing for that with 3D classification.
Obvious tutorial! Could you give more information on the threshold of 1.27? How can I determine the accurate number?
The threshold can be set to any number and can be found by looking at the the contouring level in the volume viewer of chimera. It will be different for every mask you make. You will find this number next to "Level".
when finding the center of mask, was it pixel-to-angstrom conversion? why did you divide, but not multiply, by pixel size?
I don't think the tutorial is not clear, but this is Chimera not ChimeraX. The extract density function in ChimeraX is not available yet, but it works in Chimera. 🤣
Hi. I am trying to work with negative stain images. I save them as tiff and convert to mrc then import. However when I open them to pick particles they look much worse than the actual image. It looks like their contrast has increased a lot and lots of features are lost. Do you have any idea why this happens? Thank you.
It is likely the default low pass filter in RELION. Try changing it from 20 to a lower number and compare.
@@cryoemtutorials5598 thank you so much
just wanted to say you're awesome and thank you for the guides!
audio missing after 50s
Thanks for sharing!
Hi, these are very useful videos for beginners. would you share your next video of ab initio and so on.
Hi, where is the next video you are talking about ab Initio task?
Oh.. There is no audio for this video..
Thanks It helps a lot. What is the next step? How to combine the maps for model building?
It's lovely to see fltk in action again. ;)
How can you get rid of the bad micrographs after ctf estimation?
hi, how at the end can i visualize the classes? how i can process multiple extraction files in a single 2D classification job?
how i create a stack containing the extraction of different images?
hi, can i pick and extract particles from tiff immages?
just to confirm, I think the coords given by chimera measure center is in angstroms instead, that makes ur calculation right to give pixels for cryosparc input. Thanks for the tutorial!
Why does the audio disappear?
Thanks for these videos. They are very helpful in learning to operate with SerialEM. For this video the sound seems to be missing. Could you re-upload that video again? Thanks Ferdinand
Thanks for letting me know. It seems like the audio has been randomly lost from all of my videos.
@@cryoemtutorials5598 For me it works for several other ones from that play list, e.g. "Preparing a Reference Image in Serial EM".
I‘m a beginner of cryo-em data processing. Your video help me a lot. Thanks.谢谢
Glad it was helpful!
Thanks for your videos they are really helpful could you please make a video about how to install RELION 3.1 with GUI I tried to follow the instructions but I really got stuck so I really appreciate if you could make a video to how install relion from scratch
Yes, That would be very useful
Yes That I need to know as well
Hi why did you stop at this?
I've been busy! New videos are out now though. Feel free to request certain topics.
Thanks for sharing the videos. But only this video has sounds, which is great.
Sorry about that, I'm not sure what happened. New videos are up with sound.