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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:

Each mode may have additional options, detailed below. See also: color bynucleotide, cartoon, hbonds, struts

nucleotides  atom-spec  atoms
– or –
~nucleotides  atom-spec 
Remove special representations to reveal atoms and bonds.
nucleotides  atom-spec  ladderradius  r ] [ showStubs  true | false ] [ baseOnly  true | false ] [ hideAtoms  true | false ]
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. Each half-rung (whether connected or not) is colored to match the C2 atom of the corresponding residue. 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.

nucleotides  atom-spec  stubsradius  r ] [ hideAtoms  true | false ]
stubs
Show nucleotide sidechains as disconnected half-rungs of the specified radius (default 0.45 Å), each colored to match the C2 atom of the corresponding residue. 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).
nucleotides  atom-spec  tube/slabradius  r ] [ shape  box | muffler | ellipsoid ] [ dimensions  small | long | big | fat ] [ thickness d ] [ hideAtoms  true | false ] [ showOrientation  true | false ] [ glycosidic  true | false ]
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: The choices for dimensions also specify the location of the slab: Each slab is colored to match the base C2 atom and each tube to match the ribose C1' atom. 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.
nucleotides  atom-spec  slabshape  box | muffler | ellipsoid ] [ dimensions  small | long | big | fat ] [ thickness  d ] [ hideAtoms  true | false ] [ showOrientation  true | false ]
slab
Show ribose atoms, but 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. Each slab is colored to match the base C2 atom. The hideAtoms option indicates whether to hide base atoms/bonds (default true).

UCSF Resource for Biocomputing, Visualization, and Informatics / July 2018