I have reached 3.x A with C1 symmetry. Thus I created a new refinement packages out of last C1 3D results but change the symmetry from C1 to C2(or D2), then run refinement again. Somehow the 3D refinment totoally messed up and looks NOT correct at all. I am wondering what's goes wrong.
You will have to first align the previously created reconstruction with your symmetry axes. You can use the tool
align_symmetrythat is part of cisTEM and can be found in the
bindirectory. Use it on your final reconstruction (wich should be in the
Assets) and import the output of
align_symmetryback into cisTEM (Import option in Volume Assets). Then use this reconstruction as your reference in Auto Refine or Manual Refine. If you use Manual Refine, you will have to perform a single round of Global Search to align all particles to the new reference (Auto Refine performs global searches automatically).
It's maybe also worth noting here, that if you do an ab-inito with symmetry, the symmetry alignment will be done for you, and the resulting model should already be aligned to the symmetry axes and have symmetry imposed.