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.
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