Angle, shift conventions

Submitted by Unknown on Tue, 2009-12-15 10:47

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Frealign

I am putting together a table of differences between 2-D alignment operations for different EM processing packages. Would you please inform me of the following conventions used in the Frealign projection-matching based refinement algorithm:

1) In which direction does inplane rotation proceed? (e.g. positive = counterclockwise) ???
2) in which direction do shifts proceed? (e.g. +x = right, +y=up) ???
3) when performing a particle alignment to a projection, what is the order of operations? (e.g. rotate, shift, mirror) ???

niko Tue, 2009-12-15 10:49

Here are the Frealign conventions. The directions I use here assume that the particle image origin is in the lower left corner (as is the case in the program Ximdisp).

1) In-plane rotation (PSI angle in Frealign): A positive value describes a counterclockwise rotation of the particle. To align it with the reference, the negative value of this angle needs to be applied, i.e. a clockwise rotation.

2) X,Y shifts: Positive values describe shifts to the right and up. The negative values have to be applied to align the particle with a reference.

3) Frealign applies the shifts first and then the rotations. There are no mirrors used in Frealign.