[3dem] "Recenter" option in Relion during particle extraction

[Iozzo, Yuri /US]

Hi everyone,
I wonder if someone can explain or can point me to a good description to understand the "recenter" option when you extract the particles in Relion. After years of use I am not sure what exactly it does.
Here is my experience with it:

  *   If I do not use any offsets for particle extraction and for my starting reference MRC file then I get a reconstruction usually close to the coordinates of starting reference,
  *   If I use XYZ (which represent the difference between voxel center and map's center of mass) offsets for extraction and still use the same starting reference then I get a perfectly centered reconstruction, although it is very distorted and compressed relative to what it should be,
  *   If I use XYZ offsets for extraction and also apply them to my starting reference (for example: "relion_image_handler --i reference.mrc --o reference_xyz.mrc --shift_x x --shift_y y --shift_z z" or "relion_image_handler --i reference.mrc --o reference_-xyz.mrc --shift_x -x --shift_y -y --shift_z -z") then the resulting reconstruction does not make any sense.
Is there any clear answer preferably with an example about when the Recenter option is useful?
Thanks,
Yuri Iozzo
Sanofi

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