Wrong alignment after re extraction

[hsosa]

Dear CS community

I want to re-extract a set f particles but the alignment of the re-extracted particles seems to be messed up and I am not sure what I am doing wrong

I have a volume and associated particles that are the result of a symmetry expansion job and subsequent volume alignment (re-centering), downsamplig (cropping) , 3D classification and local refinement jobs . I have then given this set of particles as input to an extraction job with the option recenter_using_shifts ON. I then did as a test a homogeneous reconstruction of the re extracted particles. I would have though that this volume will be identical to the original volume/particles I used for the re-extraction job as they have the same alignment etc but this is not the case.

How should I proceed? Is the problem related to the symmetry expansion or the volume alignment (re-centering) jobs?

Thanks

H.

[olibclarke]

What CS version are you using?

Wondering if the downsampling in your workflow may be causing the issue:

Recentering when downsampling does not update particle locations

When using the “Downsample particles” job with the “Recenter using aligned shifts” setting enabled, the resultant .cs file shows that the alignment shifts are reset to sub-pixel values (presumably to match the new images), but the particle coordinates/locations are not updated. Thus if these are later re-extracted, or the original particle.blobs are attached, they reconstruct with the original centre but with loss of aligned shifts, resulting in a poorly aligned average. This is particularly ap…