I have a C2 symrtric complex. By masking one end in 3d classification, I can identify several conformations, but in any one state the other end is a mixture of states (uncordinated conformasional chages despite C2 structural symetry).
I’d like to be able to use 3d classification seperatly on both ends, identify the same conformation, then average those two 1/2 structures together, to provide the best resolution for that conformational state. Does anyone have an idea on how to do this in Cryospark?
Essentially, I wish to treat the two halves of the C2 complex as indipendent particles.
It sounds like what you want to do is first perform C2 symmetry expansion (after refining with C2 symmetry enforced), then local refinement with a mask around one protomer, followed by focused 3D classification
@olibclarke, thanks for that advice, that is interesting. I’m just trying to understand your logic: Why would it be important to refine with C2 symmetry enforced before doing c2 symmetry expansion? Also I don’t understand why the local refinement with the mask around the one protomer would need to be in the workflow?
Would you expect similar results from just C2 expansion followed by 3d classification with a focus mask on the single protomer?
It really depends on the nature of the asymmetry. If the complex is more or less C2 symmetric, but with differences in some parts, refining with C2 symmetry will improve resolution & quality of alignments, at the expense of degrading the map in the areas that differ. In any case the complex needs to be aligned with the C2 axis on Z prior to symmetry expansion.
I suggest local refinement prior to classification assuming that there is some flexibility between the two protomers; if this is not the case, then just doing sym expansion followed by focused classification should also work fine