Some of us actually noticed this conventions issue a ways back (one of the classic EM test
samples, the T20S proteasome, has D7 symmetry), but I thought it had been fixed already. Seems like I am mistaken…
We have been converting refinement cs files to star files (using pyem). Our particle has D7 symmetry and in our later reconstructions (using relion or xmipp) were rendering a D14 symmetry. We have looked into this in more detail and we believe that cryosparc defines Dn as Cn around z + C2 around Y, while relion and xmipp, and maybe others, define it as Cn around z + C2 around X.
Therefore, pyem 3d angles conversion is not a straightforward conversion, at least for Dn symmetries.
We think the…
opened 07:11AM - 02 Jul 19 UTC
closed 11:54PM - 28 May 20 UTC
bug
Hi, @asarnow thanks for having this nice repo.
We are actually using it and we… were converting cs output to relion star file using this (actually what is in pipy).
Later we did a reconstruction with relion and xmipp and both didn't seem right. Our refinement in CS has a D7 symmetry whereas both reconstructions (relion and xmipp) showed a D14 symmetry (in both cases we specified D7 symmetry fro the reconstruction.
Does it ring any bell?
Alternatively....do CS offer an equivalent to relion_reconstruct, I mean asking CS to make a reconstruction using angle in a star file?