===== Signal subtraction =====

==== What do I need? ====
This protocol assumes that you have run Meridien.

==== Steps ====
  ; [[avgfilt|Average and Filter]] : Average and low-pass filter a map for segmentation.
  ; [[segment|Segment Filtered Map]] : Display the map in Chimera, and locate regions to be subtracted.
  ; [[sp_mask|Generate and Apply Mask]] : Make a soft mask of the region to be excluded.
  ; [[projsubtract|Project and Subtract]] : Compute re-projections of map to be subtracted, and subtract them from the original images.
  ; [[pipeline:meridien:sxmeridien|Compute 3D Reconstruction]] : Compute a 3D reconstruction using refinement iteration used for signal-subtraction.
  ; [[centershift|Center Map]] : Center map of remaining density.
    
==== What do I do next? ====
Once these steps have been completed, perform a restricted refinement.

\\
==== Author / Maintainer ====
Tapu Shaikh

Based on protocol developed by Zhong Huang and Pawel Penczek

==== Reference ====
Bai XC, Yan C, Yang G, Lu P, Ma D, Sun L, Zhou R, Scheres SHW, Shi Y. (2015) "An atomic structure of human γ-secretase." //Nature// **525**: 212-217. doi: 10.1038/nature14892.