Definition of particle origin
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The PFT3DR convention for origins is the pixel distance from the first pixel of the image. To get shiftx and shifty, do I simply subtract the "center" of the box from the origin? In other words, if my image box is 100 x 100 pixels ("center" at 51,51?, I assume from NSAMP/2 + 1) and the particle origin at 51.3,49.4, would the shifts be
51.3 - 51 = 0.3 and 49.4 - 50 = -1.6?
Yes, the particle origin in
Yes, the particle origin in Frealign is assumed to be N/2+1. For a 100 x 100 pixel image, this would be 51,51. The shifts expected in a Frealign parameter file are those that describe the current state of the particle, not the shifts that need to be applied to recenter it. So if a particle origin is at 51.3,49.4, the correct shifts in the Frealign parameter file should be as you calculated: