The nucleotides command generates special representations of nucleic acids, with choices for mode:
Each mode may have additional options, detailed below. See also: color bynucleotide, cartoon, hbonds, rungs, struts• nucleotides atom-spec atoms
Remove special representations to reveal atoms and bonds.• nucleotides atom-spec ladder [ radius r ] [ stubs true | false ] [ baseOnly true | false ] [ hideAtoms true | false ]
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 such connections will be shown as half-rungs if stubs is true (default), otherwise omitted from the ladder representation. The rungs attach to cartoon at the C3' tether position, and stubs end at the nucleic acid base N1 (if purine) or N3 (if pyrimidine). 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. Each half-rung is colored to match the cartoon of the corresponding residue. The hideAtoms option indicates whether to hide atoms/bonds for nucleotides shown as rungs (default true).• nucleotides atom-spec tube/slab [ radius r ] [ shape box | muffler | ellipsoid ] [ dimensions small | long | big | fat ] [ thickness d ] [ hideAtoms true | false ] [ showOrientation true | false ] [ glycosidic true | false ]
Although the ladder represention can be limited to specified residues, the ladder settings are per-model (e.g., different residues in the same model cannot have a different rung radius). See also: rungs
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:• nucleotides atom-spec slab [ shape box | muffler | ellipsoid ] [ dimensions small | long | big | fat ] [ thickness d ] [ hideAtoms true | false ] [ showOrientation true | false ]
The choices for dimensions also specify the location of the slab:
- box (default) - rectangular box
- 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)
Each slab is colored to match the nitrogen at one end of the glycosidic bond, and each tube to match the ribose carbon (C1') at the other end. 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:
- 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 bondDifferent residues can have different slab parameters.
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.
Represent bases as slabs of the specified shape, dimensions, and thickness (default 0.5 Å), optionally with showOrientation bumps, as described above for nucleotides slab. Each slab is colored to match the base nitrogen involved in the glycosidic bond. The hideAtoms option indicates whether to hide base atoms/bonds (default true).