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.
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