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StochasticAnalytics / emClarity

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tilt angle for empiar 10064 #135

Closed yuanhaowang1213 closed 3 years ago

yuanhaowang1213 commented 3 years ago

Hi,

I was trying the code for empiar 10064, but unfortunately it seems it did not contain the tilt angles inside the data. So may I ask what is the tilt angle setting for the data mixedCTEM you used in your paper?

Regards,

bHimes commented 3 years ago

If I remember right, the tilt angles are in the methods section of the original (Khoshouei et al)

yuanhaowang1213 commented 3 years ago

Not really. They said the max/min angle is 60/-60, with 2 degree increment. However, in the data mixedCTEM, there are only 58 or 59 tilts, not 61, so it is wired. I checked with the last author, but unfortunately, he could not get access to the original data. So I want to try whether you have the original setting for the paper or not.

Regards,

bHimes commented 3 years ago

If you play the tilt series in imod, is there one side that is clearly at a higher tilt angle? I probably based my tilt angles off this sort of visual inspection. Anyway, a constant offset of a couple of degrees shouldn't hurt too much - it will only create a small error in CTF correction for higher tilts, which only contribute at lower resolution anyway. Not ideal, but for these data, it is acceptable IMO.

Benjamin Himes, PhD

cryoEM methods development HHMI, RNA Therapeutics Institute, University of Massachusetts Medical School

cryo-STA development @ emClarity https://github.com/bHimes/emClarity Visual Proteomics @ cisTEM https://github.com/timothygrant80/cisTEM

On Wed, Apr 28, 2021 at 10:53 AM Yuanhao Wang @.***> wrote:

Not really. They said the max/min angle is 60/-60, with 2 degree increment. However, in the data mixedCTEM, there are only 58 or 59 tilts, not 61, so it is wired. I checked with the last author, but unfortunately, he could not get access to the original data. So I want to try whether you have the original setting for the paper or not.

Regards,

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yuanhaowang1213 commented 3 years ago

Thank you for your experience. I tried and it worked.

bHimes commented 3 years ago

No worries - good luck!