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Main topics:

- ARB: a Short Introduction
- Glossary
- Visualization of Three-dimensional structure of small subunit (16S) rRNA

Related topics:

# Display options for the Residues / Bases

- OCCURRENCE
- DESCRIPTION
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## 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