half-tomograms

[Jason K]

Dear EMAN2ers,

We are finding that denoising based on even/odd half-tomograms has some dramatic & useful effects on our in situ datasets. The typical way of producing these half-tomograms is by using every other frame from the raw movies. Ideally, one could preserve the (frame/frame and tilt/tilt) alignments and map them back to the raw data to reconstruct these. Is there an implementation of this in EMAN2 floating around that I am not aware of, and if not, are there any things that would be good to keep in mind before I try to kludge together something?

Thanks,

Jason Kaelber

[Muyuan Chen]

If you use every other frame, presumably you can create half tilt series quite easily. Then assume the alignment parameters for the two tilt series are the same, I think you can just rename the tilt series as “titlseries/xxx__even(odd).hdf”, and run e2tomogram with “—load —notmp —niter 0” for both files, so it will generate the even/odd tomograms with the alignment from the original tilt series. Since EMAN2 considers files with labels after the double underscore “__” the same, it should automatically load the correct metadata. The only issue is it will write to the same tomogram file name and overwrite the files. So you will just need to rename the tomograms correspondingly. 

I think this should work. I may have done it years ago but I don’t have an actual program for this. 

Muyuan

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[Ludtke, Steven J.]

We've been doing this recently to assess the resolution of tomograms (even/odd splits on the aligned tilt series), but we don't have a pipeline for it to be done routinely right now. As Muyuan said, the only real trick is to make sure you use exactly the same alignment parameters on the two tomograms so they are in identical orientations.

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center