output image stack with applied .par parameters?

Submitted by Jma25 on Tue, 2015-08-11 08:15

Forums

Frealign

Hi Niko,

Is there any way to apply the parameters in the .par file (I am using an old version 8) to the frealign image stack (spider in this case) to create an output aligned image stack?
If I can not do this directly inside frealign, I suppose I would have to convert the par file.. any suggestions?

This is so that I can do 2D classification (would have to be outside of Frealign) to remove junk particles.

Cheers,
Joe

niko Tue, 2015-08-11 14:43

The PSI angles in the Frealign parameter file provide the in-plane angles that need to be applied to the particles to align them. Using these as well as the X,Y shifts should give you the information you need to align the particles using Spider. The angle and shift conventions of Frealign and Spider are the same. However, they might differ in their sign. You will have to reformat the PSI angles and X,Y shifts into a Spider document file and test if the parameters rotate and center the particles correctly. If not, try the negative values of the PSI angles and/or the negative values of the X,Y shifts.