Hi,
> That way in 3.0 solvent area was not touched during subtraction. In 3.1 this is not clear - it looks like we need to provide just a usual mask covering area of interest. Then if the second, larger, mask is taken from the optimiser file, then the solvent will not be touched either, but if not, the solvent area in the maps from optimiser file will be subtracted from each particle. Which option is in fact used in 3.1?
>
> If mask from optimiser is not used, was it decided that subtracting solvent is not a problem or may be it will be beneficial to provide now a mask covering area of interest plus solvent?
The mask in optimiser.star is not used by subtraction
itself. It is used only to find paths to half maps.
However, the half maps might have been already masked
if you used "Use solvent flattened FSC" in the
Refine3D job. In this case, solvent regions
are zero, so they are not subtracted.
Best regards,
Takanori Nakane
> Also, presumably the optimiser file should be from the last iteration in auto-refinement or are there any other considerations?
>
> Many thanks for info!
>
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