Wrong reconstruction using Reconstruct tomograms (Discrepancy with AreTomo)

[navya19j]

Describe your problem

I am interested in using Relion to reconstruct a set of aligned tilt series. I have a stack of aligned tilt series (from AreTomo) and also an alignment file (.aln). I use these files to modify the input to the job Reconstruct tomograms. The modified file looks like the below,

I only update _rlnTomoXTilt, _rlnTomoYTilt, _rlnTomoZRot, _rlnTomoXShiftAngst and _rlnTomoYShiftAngst and _rlnMicrographName, all according to Aretomo's alignment file. However, if I use this modified star file as an input to the job Reconstruct Tomograms, it gives me a wrong reconstruction. The obtained reconstruction is not only low in contrast but also differs significantly from the one obtained through AreTomo

Reconstruction from AreTomo

Reconstruction from Relion

The motivation behind doing this primarily a difference in the reconstructions obtained after following the entire pipeline from Import in relion and using AreTomo. I have a set of particle picks in the AreTomo reconstructed tomogram and in order to map them back correctly for subtomogram averaging, I need a way to make the two reconstructed tomograms similar.

For reference, this is the reconstruction from Relion after following the entire pipeline, (which differs significantly from AreTomo, both in terms of contrast and Z shifts)

Any help/insight will really be helpful. Been on it for a while now.

Thanks
Navya