Coordinates in tilt-series

[Reza Khayat]

Hi,

I have picked particles from the tomograms and notice that the particles move in the low tilts and are missing in the high tilts. I don't see how sub-tilt refinement could fix the problem if the particle is not present in the stack. Thus, is it possible to printout the coordinates for each tilt of a tilt-series? My particles are large (70nm) and identifiable in the tilt series. 

Best wishes,
Reza

[Muyuan Chen]

I think those particles will be automatically skipped when you extract particles. You still get the 3D particles, which are reconstructed by fewer 2D images. The corresponding 2D particles at high tilt simply do not get generated, therefore never get refined by the subtilt alignment.

So, if you really want the coordinates, for the 2d particles that were written down, they are in particle header under the key “ptcl_source_coord”. But they don’t exist for those that never got written down. You can figure it out with some coding with reference from e2spt_extract.py.

Muyuan

On Apr 5, 2026, at 11:25 AM, Reza Khayat <khaya...@gmail.com> wrote:

Hi,

I have picked particles from the tomograms and notice that the particles move in the low tilts and are missing in the high tilts. I don't see how sub-tilt refinement could fix the problem if the particle is not present in the stack. Thus, is it possible to printout the coordinates for each tilt of a tilt-series? My particles are large (70nm) and identifiable in the tilt series. 

Best wishes,
Reza

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[Reza Khayat]

Hi Muyuan,

Thanks so much for quick respond. I see that em2info.py --all -H particles/XXXXX.hdf will print out ptcl_source_coord information I need. I can write code/script now. 

Berst wishes,
Reza