Combination of right-handed and left-handed maps

3D Reconstruction
1

Hello,

I ended up two different maps which are mirrored to each other, one of them has right-handed helices while the other one has left-handed helices.

I see the differences even in the 2D classification and 3D classification jobs. Then I had two different maps with slightly similar resolutions at the end.

My questions are;

  1. Is it possible to see left-handed features during the 2D and 3D classifications?
  2. Does the combination of right-handed and left-handed maps make improvement in resolution?

Thanks!

2

This is normal. Your particles are projections of the individual protein molecules, and the projections do not have intrinsic handedness - they are equally (almost!) compatible with both left & right-handed solutions, so in ab initio reconstruction, you have equal chances of converging on the correct (right-handed) or inverted (left-handed) solution.

If you have multiple classes which are identical except for the handedness, you can just pick one which has the correct handedness and use that for subsequent refinement/classification.

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3

Many thanks for your prompt response!

So, would combining all the particles, then flipping the map if left-handed cause having duplicate particles? Would it improve resolution? or using classes with the correct hand is the correct way to do as you suggest?

Thanks!

4

There should not be any duplicate particles. You can use the particles from all the well resolved classes that only differ by their handedness, and just refine against a single volume with the correct hand.

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