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![[Figure 5]](id5015fig5mag.jpg)
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Figure 5
Interactive segmentation and contextual density control with SURFER in UCSF ChimeraX. (a) ChimeraX interface illustrating SURFER applied to the γ-secretase complex (EMDB entry EMD-3061). The averaged unfiltered map is shown in grey, with the outline of the FDR-based confidence mask superposed. (b) Close-up of the SURFER tool interface. SURFER accepts a pair of unfiltered half maps as input and optionally a molecular boundary mask. Predicted micelle density can be visualized across a range of binarization thresholds. Once a threshold is selected, the segmented micelle can be subtracted from any target map aligned to the raw input. In this example, a LocScale-FEM optimized map (Bharadwaj et al., 2025  ) is used as the target. (c) LocScale-FEM target map, SURFER-predicted micelle density and the corresponding micelle-subtracted map for EMDB entry EMD-3061. (d) Application of SURFER to the relaxin family peptide receptor 4 (EMDB entry EMD-33888). Shown are the raw map, the deposited DeepEMhancer-optimized map and the LocScale-FEM map before (top) and after (bottom) micelle subtraction. Density corresponding to the bound RXFP4 ligand is preserved in the subtracted map. (e) Application of SURFER to the connexin43 (Cx43/GJA1) gap-junction intercellular channel (EMDB entry EMD-33394). A LocScale-2.0-optimized target map is shown before and after micelle subtraction. Density associated with tightly bound lipids is retained in the micelle-subtracted map but its retention depends on the chosen binarization threshold. |
![[Figure 5]](id5015fig5.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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