Heterogenous refinement for a part of complex-how to use half maps?

Hi all,
I have refined a multi protein complex to 3.5A resolution using relion. I want to try cryosparc heterogenous refinement but only for a part of complex that is poorly resolved and likely have more heterogeneity. However I’m not sure how to use the half maps. Can I delete the unwanted parts from the half maps in Chimera and use as an input for heterogenous refinement.


masked heterogeneous refinement is not supported at present - this will only work if you perform signal subtraction first

Thanks Oli,
I forgot to write, I have signal subtracted particles but how to use the half maps? If I use full maps I get no meaningful results for the part I am interested in.

by half maps you mean maps with only your part of the complex? Perform a reconstruction from the subtracted particles - use the Homogeneous Reconstruction job type

then you can use this as an input for heterogeneous refinement

However in my experience classification without alignments in relion will probably give better results for this particular scenario

1 Like