focused refinement with signal subtraction

[Madeline Rollins]

Hi,

Is it possible to do focused refinement without including the density for other subunits for the subtomogram averaging pipeline in EMAN2?

 

I found this documentation that describes two approaches for looking at a single subunit at a time for symmetric particles:

https://blake.bcm.edu/emanwiki/EMAN2/TomoSymmetry

 

One of the approaches is to re-extract the particles centered on a subunit, where you have reduced the box size and provide the appropriate 3D translation.

Is there a simple way to do something like this without re-extracting particles for something that has no symmetry (C1)? For example, would using --maskalign in the e2spt_refine_new command be sufficient?

All the best,

Madeline

[Muyuan Chen]

Yes. It works as long as the subunit you focus on is not too small. One example here. 

https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_p22#Tail_refinement

Compared to the guide in the tomosymmetry link, one difference here is we start the refinement with "e2spt_gathermeta.py". This uses the subtilt alignment information from the full particle refinement, which helps  sometimes if you want to reach higher resolution.

Muyuan

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[Madeline Rollins]

Thanks, I will try this now. If I wanted to "unsubtract" the other densities to have an unmasked, locally filtered map, could I just add the threed_even/odd_unmasked.hdf files? Or do I need to copy the threed_raw_even/odd.hdf and then run e2refine_postprocess?

Madeline

[Muyuan Chen]

It may be better to run e2refine_postprocess so you get the filtering properly, but in principle, just adding the even/odd_unmasked file shouldn't hurt. 

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