Unfiltered refined map for LocScale

3D Refinement
1

Hi,

I would like to use LocScale to sharpen my cryosparc map from local refinement using my current refined model as a reference. An unfiltered, unsharpened map is required by LocScale. From previous posts on this forum I understand that the half-maps are unfiltered. Is the volume_map.mrc file also unfiltered?
UPDATE
I just tried LocScale using the volume_map.mrc file from cryosparc and it gave much poorer features in the output LocScale map than when I run it with a volume_map_half_A.mrc file. Does that mean the former is filtered? If so, how can I generate an unfiltered full map?

Regards
Lizelle

2

Hi @lizellelubbe,

This is correct; the full volume_map output will have high-res fourier components downweighted by the FSC. The half-maps are unfiltered, so the easiest way to get a full, unfiltered, unsharpened map is by adding together the two half maps (map_half_{A,B}.mrc), which could be done for e.g. in Chimera using vop add.

Best,
Michael

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3

Thanks for the help Michael!

4

Or with emcalc.py from pyem:

emcalc.py "(a+b)/2" halfA.mrc halfB.mrc avg.mrc

Though presumably the factor of 2 doesn’t matter.

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