Hi, a 100KDa complex form a fible. With “Order 5, Rise 51.18A, Twist 136.98“, Helix Refine reach 2.61A, which is good enough to dock atomic model. The repeat unit has two 100kDa complex, with obvious C2 symmetry. NU-refine with C2 symmetry got higher resolution than C1, but Helix Refine with C2 produce low resolution and wrong reconstruction. How to apply C2 symmetry within Helix Refine?
when you say there is C2 symmetry, you mean within the asymmetric unit of the helix? In that case, you probably want to apply helical symmetry expansion, align the C2 axis to Z, then run local refinement with C2 symmetry applied
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Depending on how it looks, you could try to impose a “pseudo-screw” symmetry; i.e. C1 with half the rise and a different twist based on 180 - [angle] rather than the previous parameters. This works a lot for amyloids (but not always).
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Thanks! I apply helical symmetry expansion, local refinement with C1 got 2.26A resolution. When I try “Vol Align Tools“, there are many options. I tried several time, and run local refinement with C2 symmetry, but the map is wrong. Maybe some options are wrong when I try “Vol Align Tools“. How to do “align the C2 axis to Z“?
