Command: nucleotides

Usage:
nucleotides atom-spec mode mode-options

Usage:
~nucleotides atom-spec

The nucleotides command generates special representations of nucleic acids, with choices for mode:

• atoms – atomic representation, no special representations; undo the other modes (same as ~nucleotides)
• fill – atomic representation, but with filled rings
• ladder – continuous or broken rungs depending on hydrogen bond pseudobonds
• stubs – broken rungs
• tube/slab – tube representation of ribose, slab representation of bases (box, muffler, or ellipsoid shape)
• slab – filled-ring atomic representation of ribose, slab representation of bases

Each mode may have additional options, detailed below. Nucleotide representations are colored according to the ring fill color of each residue.

See also: preset, color bynucleotide cartoon, style, aniso, hbonds, struts, Actions menu, Nucleotides icons

Remove special representations to reveal atoms and bonds.

slab

Atomic representation, but with filled rings (base and ribose). Fill thickness can be adjusted with style.

ladder Show nucleic-acid residue pairs connected by hydrogen bond pseudobonds as rods or ladder rungs of the specified radius (default 0.45 Å). Nucleic acid residues without H-bonds to others will be shown as disconnected half-rungs if showStubs is true (default), otherwise omitted from the ladder representation. If baseOnly is true (default), connecting rungs will only be drawn for H-bonds between base atoms; if false, thinner connecting rungs (radius 0.2 Å) will also be drawn for H-bonds involving non-base atoms. The rungs attach to cartoon at the C3' tether position, and disconnected half-rungs (stubs) end at the nucleic acid base N1 (if purine) or N3 (if pyrimidine). The hideAtoms option indicates whether to hide atoms/bonds for nucleotides shown as rungs (default true).

Although ladder/stub representions can be limited to specified residues, the associated parameters are per-model: e.g., different residues in the same model cannot have a different rung radius.

stubs Show nucleotide sidechains as disconnected half-rungs of the specified radius (default 0.45 Å). The rungs attach to cartoon at the C3' tether position, and the stubs end at the nucleic acid base N1 (if purine) or N3 (if pyrimidine). The hideAtoms option indicates whether to hide the corresponding atoms/bonds (default true).

Represent ribose moieties as tubes of the specified radius (default 0.2 Å) and bases as slabs of the specified shape, dimensions, and thickness (default 0.5 Å). The shape can be:

• box (default) – rectangular box
  box muffler ellipsoid
• muffler – rectangular in the plane of the base, oval in cross-section (large enough to enclose the corresponding box)
• ellipsoid – oval in the plane of the base and oval in cross-section (large enough to enclose the corresponding box)

The choices for dimensions also specify the location of the slab:

• small (default for ellipsoid shape) – anchored at the base end of the glycosidic bond
• long (default for box and muffler shapes) – anchored at the base end of the glycosidic bond
• big – anchored at the ribose end of the glycosidic bond (C1')
• fat – anchored at the ribose end of the glycosidic bond

The hideAtoms option indicates whether to hide nucleotide atoms/bonds (default true). The glycosidic option applies only to base-anchored slabs (dimensions small or long) and controls whether the ribose tube should connect to the glycosidic bond (if true) or directly to the slab (false, default). The other end of the tube is the average of the C3' and C4' atom positions. The radius setting applies only to the tube, not the glycosidic bond that remains visible with glycosidic true; the stick radius of the bond can be changed separately with the size command. The showOrientation option (default false) indicates whether to show the positive faces of bases with bumps on the slabs. These faces point towards the 3' end of a strand in right-handed A- and B-DNA, along the positive Z direction described in:

showOrientation bumps

A standard reference frame for the description of nucleic acid base-pair geometry. Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu XJ, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung CS, Westhof E, Wolberger C, Berman HM. J Mol Biol. 2001 Oct 12;313(1):229-37.

Different residues can have different slab parameters.

slab

Show ribose as atoms with ring fill and represent bases as slabs of the specified shape, dimensions, and thickness (default 0.5 Å), optionally with showOrientation bumps, as described above for tube/slab display. The hideAtoms option indicates whether to hide base atoms/bonds (default true). Ribose ring-fill can be turned off or its thickness adjusted with style.