Results for 5gjw

PDB: 5gjw Gene name: CACNA2D1 UniProt: CA2D1_RABIT EMD: emd_9515.gz
EMD-9515

Membrane mimetics: micelle; digitonin Note: More manual adjustment needed because of the noise level

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

* end0 around -25 5
* end1 around 25 5

Boundary values (averages for MemBlob)

	Z (PDBTM)	Z (MemBlob)	Z - 8
End1	15.05	25.89	17.89
End0	-15.05	-29.22	-21.22

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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