This protocol assumes that you have run Meridien.

Average and Filter

Average and low-pass filter a map for segmentation.

Segment Filtered Map

Display the map in Chimera, and locate regions to be subtracted.

Generate and Apply Mask

Make a soft mask of the region to be excluded.

Project and Subtract

Compute re-projections of map to be subtracted, and subtract them from the original images.

Compute 3D Reconstruction

Compute a 3D reconstruction using refinement iteration used for signal-subtraction.

Center Map

Center map of remaining density.

Once these steps have been completed, perform a restricted refinement.

Tapu Shaikh

Based on protocol developed by Zhong Huang and Pawel Penczek

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.