Results for 3j9j

PDB: 3j9j Gene name: Trpv1 UniProt: TRPV1_RAT EMD: emd_5778.gz

Membrane mimetics: amphipol; DDM, soybean lipids, then prt:amphipols (1:3 ), then detergent was removed and for cryo-EM detergent was replaced by amphiols

Cross-sections at different angles

green: density, gray dots: atoms from the all-atom model, lines: membrane boundaries defined by TMDET

The determined edges at each slice and their comparison to TMDET

dots: edges of the gradient, triangles: outliers,
dashed and solid lines: membrane boundaries defined by TMDET and MemBlob ( mean(Zi) decreased by the thickness of the interface region (8 Å))
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Manual settings applied


Boundary values (averages for MemBlob)

Z (PDBTM) Z (MemBlob) Z - 8
End1 15.50 16.89 8.89
End0 -15.50 -18.44 -10.44

Mapping the results to the structure

You can move/scale/rotate the structure. Blue: a.a. facing to bulk water; magenta: interface region; green: a.a. interacting with the hydrophobic membrane core; yellow: burried a.a. red: a.a. with an invisible side chain and non-protein molecules, for which DSSP cannot return SASA
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