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Command: rungs

rungs  atom-spec  [ radius r ] [ color color-spec ] [ halfbond  true | false ] [ hideAtoms  true | false ] [ hideHbonds  true | false ] [ showRibbon  true | false ]

~rungs | rungs hide )  atom-spec

The rungs command shows a simple broken-ladder representation of the nucleic acid residues containing the specified atoms, or if nothing is specified, all nucleic acid residues. A pseudobond model named rungs is created, in which the rung for each residue is a pseudobond from the ribose C3' to the nucleic acid base N1 (if purine) or N3 (if pyrimidine). The ~rungs or rungs hide command undisplays any rungs of the specified residues.

Simple rungs drawn with the rungs command may be detached from the cartoon, but special representations (including ladder rungs) drawn with the nucleotides command are cartoon-integrated. See also: cartoon, show, struts

The initial default rung radius r is 0.5 Å, and the initial default color is to match the cartoon of each residue. If halfbond is true (initial default false), the color setting is not used; instead, the two halves of each rung will be colored to match the endpoint atoms, and will track any subsequent color changes of those atoms. Parameters that are not specified retain their current values. Color and radius can be changed with subsequent uses of the rungs command or with other commands (color, size).

The hideAtoms option indicates hiding the atoms/bonds of the specified residues (default true), not including the rung endpoint atoms, which must remain shown for the rungs themselves to be shown. The hideHbonds option (default true) indicates hiding any H-bond pseudobonds. The showRibbon option (default true) indicates whether to show the ribbon (cartoon) segments of the residues. Setting a hiding option to false will not show already hidden items, and setting showRibbon to false will not hide any cartoon segments that are already shown.

Showing atoms again after hiding rungs (for example, with the command: show nucleic) may make the rungs reappear. They can be hidden without hiding the atoms by hiding or closing the rungs pseudobond model by model number.

UCSF Resource for Biocomputing, Visualization, and Informatics / December 2017