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More documentation can be found on the ARB website.
Last update on 08. Apr 2009 .
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General Dislpay 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 seq