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Hi Sandip,
These are always a bit tricky. After relion_refine and relion_postprocess, the maps get low-pass filtered, so you may not want to use those directly.
1) Use relion_image_handler to a) sum the 2 unfil.mrc half-maps; b) apply a negative B-factor; c) apply a solvent mask
2) As above, without the summation.
Then use relion_image_handler again to calculate FSC curves. The FSC is invariant to sharpening, but if you mask after sharpening, there is a small difference. As at most steps: you may want to avoid using very sharp masks that cut through the reconstructed density. You can generate soft-edged masks with relion_mask_create.
HTH,
Sjors--
On 12/08/2017 12:57 PM, Sandip Basak wrote:
Hi Everyone,
I want to make model Vs summed map and model Vs half maps. I have few questions regarding that.
1. For summed map which one I should use, Refine3d map or post process masked map? If I am not wrong the map from refine3d is not masked. Therefore, I see quite difference at resolution between fsc at 0.5 and 0.143. This is not the case for postprocesss masked map. For postprocess map resolution is very close at fsc 0.5 and 0.143.
2. For model Vs half map the problem is same. The half map is not masked. Now how to use mask only for single half map. I am using eman2 to calculate fsc. Command is e2proc3d.py A.mrc fsc.txt - - calcfsc=B.mrc.
Is there any way to use mask during calculation of fsc?
Thanks and best regards
Sandip Basak
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres