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#************* Title of helpfile !! and start of real helpfile ********
TITLE		Display options for the Residues / Bases

OCCURRENCE	In ARB primary structure editor (ARB_EDIT4) -> RNA3D

DESCRIPTION

    To achieve more performance and dynamic overlay of any sequence associated
    information, rendering (drawing) was simplified to chain display with the capacity to
    display residues in the form nucleotides - Adenosine (A), Guanine (G), Cytosine (C)
    and Uracil (U) at the respective coordinates in the molecule. Also viewing the entire
    chemical structure in the molecule’s 3D structure is less readable.

    Display Bases

            By enabling the check box the corresponding residues in the rRNA sequence can
            be displayed on the rRNA 3D structure. Disabling this check box will display
            the molecule skeleton without residues.

    Helix Region

            Enabling this check box will display residues that are participating in Helix
            formation in the secondary structure models of small subunit rRNA.

    Unpaired Helix Region

            Enabling this check box will display residues that are participating in bulge
            (unpaired helix) formation in the secondary structure models of small subunit
            rRNA.

    Non-Helix Region

            Enabling this check box will display residues that are participating in loop
            (non-helix) formation in the secondary structure models of small subunit rRNA.

    Display Size

            The size of the residues displayed can be changed by specifying the desired
            size in “Display size” box.

    CHARACTERS

            The corresponding residues are displayed with the actual nucleotides -
            Adenosine (A), Guanine (G), Cytosine (C) and Uracil (U).

    SHAPES

            The corresponding residues are displayed with the respective shapes specified
            for different structural motifs.

    By setting different colors for the secondary structural motifs (loops, stems and
    bulges) using “Color Settings”, the respective regions can be easily recognized in
    the rRNA 3D structure.

NOTES		None

EXAMPLES	None

WARNINGS	None

BUGS		No bugs known
