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#************* Title of helpfile !! and start of real helpfile ********
TITLE           RNA3D Display Options

OCCURRENCE      In Primary Structure Editor (ARB_EDIT4) -> RNA3D Program

DESCRIPTION 
        
    The following display options can be set to the three-dimensional structure of small subunit rRNA - 

    Display Molecule Skeleton

            Enabling this will display the entire molecule skeleton in a user-defined
            color. By setting a grey or light color you can achieve transparent contours
            of the molecule displayed avoiding its interference with the mapping
            information.

    SIZE:

            The size or thickness of the skeleton can be set by specifying the desired
            thickness in the “size” box. By default it is set to decimal 5.

    COLORIZE MOLECULE SKELETON:

            Based on the residues participating in secondary structural motifs (loops,
            helices, bulges) the molecule skeleton can be colored. Color settings with
            respect to secondary structural motifs can be changed using the “Color
            Palate” of the RNA3D interface.

    DISPLAY BASE POSITION:

            Base positions corresponding to the reference sequence (Escherichia coli) can
            be displayed by checking this check box. The interval of positions to be
            displayed can be changed by specifying the desired “interval size” at the
            included box. Displaying the base positions helps i) to locate probe binding
            sites within the molecule, ii) to refine the sequence alignments according to
            the molecule structure, and also iii) to identify the exact position in the
            primary sequence, where insertions, deletions and base substitutions occur
            with respect to the template sequence when a different rRNA sequence is mapped
            onto the master structure.

    ROTATE MOLECULE:

            Enabling this check box rotates the molecule automatically. The direction and
            speed of the rotation can be changed by using left mouse button and mouse
            movement, respectively. Alternatively, molecule can also be rotated by
            pressing “space bar” on the keyboard.

    DISPLAY CURSOR POSITION:

            Checking this box will enable the cursor position to be displayed in the
            molecule. Cursor position is directly connected to primary structure editor
            (ARB_EDIT4) and any movement of cursor in ARB_EDIT4 is instantly updated in
            the RNA3D window.
           

NOTES           None

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known