Loading a sequence
To load a sequence click on "Select" button from the main panel and select an
amino acid file (*.ami). Alternatively, you can copy/paste the sequence from another file.
Representation
To start the analysis, highlight a fragment of the sequence with the mouse.
By default the program will plot a helix. To view the hydrophobicity graph, please
go to "View->Hydrophobicity Graph" from the graph screen.
MB divides amino acids into 3 groups:
1.) No charge (nonpolar and uncharged polar side chains):
Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Ser, Thr,
Asn, Gln, Tyr, Cys
By default: black
2.) Posively charged chains:
Lys, Arg, His
By default: red
3.) Negatively charged chains:
Asp, Glu
By default: blue
4.) Proline
Pro
By default: green
It's also possible to change the angle between the residues, the background colors and the line
colors from the main panel.
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