Hi,
1) I have a map which was autorefined with no symmetry. The resulting structure has approximate C2 symmetry. (I.e. it's a psuedo-dimer). If I run relion_align_symmetry it finds the ~C2 axis nicely and reports the corresponding Euler angles. However, if I project the symmetry aligned map along rot=0, tilt=0, phi=0 and compare that with the projection of the original map using the angles reported by relion_align_symmetry, the 2 projections are translated slightly (~1 pixel) with respect to each other in both x and y. They seem to be identical except for this translation. Can someone please explain the origin of this and hopefully tell me how to avoid it?
2) Given the star file from the original refinement and the Euler angles from relion_align_symmetry, I'd like to generate a new star file corresponding to a the reference now having it's axes C2 aligned. Are there any command-line utilites in Relion which will do perform this transformation easily? (Certainly I can compute rotation matrices, multiply, and convert back to Euler angles if necessary. I'm just wondering if there's an easier way already provided which I've overlooked...
Thanks!
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