Chimera Commands Index

Usage:
nucleotides  sidechain  representationsidechain-options ]  atom-spec

Usage:
nucleotides  ndbcolor  atom-spec

Usage:
~nucleotides  atom-spec

The nucleotides command generates special representations of nucleotide bases and sugars; it is the command-line implementation of the Nucleotides tool. Even if only particular atoms are specified, the entire residue(s) containing the atoms will be affected. The nucleotides command does not control ribbon display. See also: aromatic, fillring, represent, ribbon, ribrepr, ribscale, ribspline, pipes, the Actions menu

The sidechain keyword indicates the base/sugar representation and may have further options:

Examples:

nuc side tube/slab shape ellipsoid style skinny orient false
nuc side ladder radius 0.35
The ndbcolor keyword specifies coloring residues by the convention used in the Nucleic Acid Database (NDB): A red, T blue, C yellow, G green, and U cyan.

The command ~nucleotides removes special representations of nucleotide residues to reveal atoms and bonds (equivalent to nuc side atoms).

Sidechain Representations and Sub-Options

The command keywords and their sub-keywords can be truncated to unique strings, and their case does not matter. A vertical bar “|” designates mutually exclusive options, and default settings are indicated with bold.

nuc side atoms
Remove special representations, including ring fill, to reveal atoms and bonds (equivalent to ~nuc). Atom/bond representations can be controlled separately (for example, with the command represent).
nuc side fill/fillorient true|false ]
Show the sugar (ribose) and base moieties as filled rings. The orient option controls whether the positive faces of bases are shown with bumps. The positive faces point towards the 3' end of a strand in right-handed A- and B-DNA (the positive Z direction in the standard reference frame). Ring fill thickness tracks the thickness of the surrounding bonds: a thin layer for wires, thicker for sticks. The thickness of sticks can be adjusted by changing the stick scale (a molecule model attribute). Regardless of the orient setting, orientation bumps will not be shown where the fill is a thin layer.
nuc side fill/slabshape box | tube | ellipsoid ] [ style big | fat | long | skinny | custom-style ] [ thickness d ] [ hide true|false ] [ orient true|false ]
Fill sugar rings and show bases as slabs of the specified shape (box, elliptical tube, or ellipsoid) and style. Elliptical tubes and ellipsoids are made large enough to enclose the corresponding box. Custom styles can be used. The default slab thickness is 0.5 Å. The hide option indicates whether to hide base atoms/bonds. The orient option controls whether the positive faces of bases are shown with bumps.
nuc side tube/slabshape box | tube | ellipsoid ] [ style big | fat | long | skinny | custom-style ] [ thickness d ] [ hide true|false ] [ orient true|false ] [ glycosidic true|false ]
Show sugars as tubes connecting the bases to the backbone, and show bases as slabs of the specified shape (box, elliptical tube, or ellipsoid) and style. Elliptical tubes and ellipsoids are made large enough to enclose the corresponding box. Custom styles can be used. The default slab thickness is 0.5 Å. The thickness of sugar tubes can be adjusted by changing the stick scale (a molecule model attribute). The hide option indicates whether to hide base atoms/bonds. The orient option controls whether the positive faces of bases are shown with bumps. The glycosidic option applies only to base-anchored slab styles (long, skinny) and controls whether the sugar tubes should each consist of a single straight segment (default) or two segments, one along the glycosidic (sugar-base) bond.
nuc side ladderignore true|false ] [ stubs true|false ] [ radius r ]
Show H-bonded residue pairs as rods or ladder rungs. The ignore option indicates whether to ignore non-base atoms when identifying H-bonds; otherwise, all nucleic acid atoms will be considered (default). The stubs option sets whether to show bases without H-bonds to other bases as half-rungs (default) or not at all. The radius (default 0.45 Å) is used for ladder rungs showing H-bonds between bases, and for stubs representing bases that lack H-bonds to other bases. When ignore is true, any H-bonds involving non-base atoms (on either or both ends) will be shown with a smaller radius corresponding to the smallest ribbon dimension, or if the backbone is not shown as a ribbon, the model stick size.

Custom Slab Styles

Usage:
nucleotides  add  custom-style  anchor  sugar|base  purine x1 y1 x2 y2  pyrimidine x1 y1 x2 y2

Usage:
nucleotides  delete  custom-style

A slab style refers to the slab dimensions and location relative to the atoms in purine and pyrimidine bases. The settings define a virtual rectangle in the plane of the base, as shown in the schematic diagrams in the Slab Style section of the Nucleotides dialog. Ellipsoid slab shapes are drawn to enclose the the virtual rectangle.

The add keyword of the nucleotides command allows defining a new custom slab style or modifying one that already exists, where custom-style is the name of the style. Custom slab styles are saved in the Chimera preferences file. The delete keyword allows removing a style from the preferences file. All arguments are mandatory for adding or modifying a style, but anchor, purine, and pyrimidine can be given in any order. Example:
nuc add square pur 0 -3.5 3.5 0 pyr 0 -2.5 2.5 0 anchor base
nuc side tube/slab style square orient false
Details:
anchor  sugar | base
Indicate whether the point of reference for the virtual rectangle should be at the sugar end of the glycosidic bond (atom C1') or at the base end.
purine  x1 y1 x2 y2
For purine bases, indicate virtual rectangle position (x1 and y1 specify the lower-left corner, x2 and y2 specify the upper right corner) in Å from the anchor; positive values are rightward along the X-axis and upward along the Y-axis in the standard reference frame.
pyrimidine  x1 y1 x2 y2
For pyrimidine and pseudopyrimidine bases, indicate virtual rectangle position (x1 and y1 specify the lower-left corner, x2 and y2 specify the upper right corner) in Å from the anchor; positive values are rightward along the X-axis and upward along the Y-axis in the standard reference frame.