Results for 3j5q
EMD-5776
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
50-70,140-150,230-250,320-350 end0 around -25 3
Boundary values (averages for MemBlob)
| Z (PDBTM) | Z (MemBlob) | Z - 8 | |
| End1 | 16.50 | 19.61 | 11.61 |
| End0 | -16.50 | -24.94 | -16.94 |
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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