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# format described in ../help.readme


TITLE		Mapping Secondary Structural Information

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

DESCRIPTION

    Secondary and tertiary structure interactions of the well established comparative
    structure models of rRNA which are used in SECEDIT to generate 2D structure models are
    fitted to the three-dimensional structure of E. coli master sequence.

    DISPLAY HELICES:

            Enabling this check box maps the secondary structural motifs (loops, helices
            and bulges) onto the molecule. Secondary structural information is according
            to the comparative models of rRNA used in primary and secondary structure
            editors.

    HELIX SKELETON:

            Enabling will draw a skeleton of secondary structure mask.  By setting a grey
            or light color you can achieve transparent mask avoiding any interference with
            other information overlays.

    DISPLAY MID-HELIX:

            This displays middle point of the helices.

    DISPLAY HELIX NUMBER:

            Checking this box will display the corresponding helix numbers in the rRNA 3D
            structure. Helix numbers are according to ARB numbering scheme.  The small
            subunit (16S) rRNA of E.coli contains 50 helices which are numbered from 1 to
            50.

    DISPLAY NUMBER OF HELICES:

            Using this you can set the number of helices you would like to be displayed in
            the 3D molecule. This feature is very helpful to thoroughly examine the
            specific helices in the structure.

    HELIX SIZE:

            Thickness or the size of the helices can be set by specifying the desired
            value in this box.

    DISPLAY TERTIARY INTERACTIONS:

            The tertiary interactions observed in small subunit rRNA can be displayed in
            the three-dimensional conformations of small subunit rRNA by enabling this
            check box. The tertiary information data is from Gautheret et al.

    Color settings related to helix, skeleton, mid-helix, helix number and tertiary
    interactions can be changed using “Color Settings” of the main RNA3D window.

NOTES
		
    Gautheret D, Damberger SH, Gutell RR: Identification of base-triples in RNA using
    comparative sequence analysis. J Mol Biol 1995, 248: 27-43.


EXAMPLES	None

WARNINGS	None

BUGS		No bugs known
