Nucleotides

Nucleotides creates special nucleotide-specific displays, including VRML representations of the base and sugar moieties. Such displays are generally combined with various atomic representations and/or ribbons. See also:

Nucleic acid visualization with UCSF Chimera. Couch GS, Hendrix DK, Ferrin TE. Nucleic Acids Res. 2006 Feb 14;34(4):e29.

• Show backbone as:
  • atoms & bonds - include all currently displayed nucleic acid backbone atoms
  • ribbon (default) - use the nucleic acid rotated residue class
  • classic ribbon - uses the nucleic acid residue class
  
  
• Show sidechain (sugar / base) as:
  • atoms & bonds - include all currently displayed nucleic acid sidechain atoms
  • fill / fill - show the sugar (ribose) and base moieties as filled rings
  • fill / slab (default) - fill in sugar rings, show bases as slabs (see Slab Options)
  • tube / slab - show sugars as tubes connecting the bases to the backbone, show bases as slabs (see Slab Options)
  • ladder - show H-bonded residue pairs as rods or ladder rungs (see Ladder Options)
  
  Before using a fill option, changing to the stick representation rather than wire is recommended so that the filled rings will have some thickness. Using the fill option for sugars creates an attribute of the sugar ring atoms named pucker, with possible values:
  • plane - defining a plane
  • envelope - outside the plane in rings with an envelope conformation
  • endo - same side of the plane as C5'
  • exo - opposite side of the plane from C5'
  Ribose rings in an envelope conformation include four plane atoms and one envelope atom, while those in a twist conformation include three plane atoms, one endo atom, and one exo atom.
  
  
• Show base orientation (true/false) - show the positive faces of bases with bumps. The positive faces are those which point towards the 3' end of a strand in right-handed A- and B-DNA (the positive Z direction in the standard reference frame). The bumps will be displayed for bases shown as slabs or filled when in the stick or ball-and-stick representation, but not for those filled when in the wire representation.

The special representations are created for only nucleic acid residues with displayed atoms, and are colored to match the atoms. Clicking NDB Colors sets atom and ribbon colors according to the convention used in the Nucleic Acid Database (NDB) Atlas: A red, T blue, C yellow, G green, and U cyan.

OK updates the display and dismisses the dialog; Apply updates the display without dismissing the dialog. The option Restrict OK/Apply... limits any changes (including setting NDB Colors) to nucleotide residues in the current selection. Close dismisses the dialog, and Help opens this manual page in a browser window.

Nucleotide displays other than atoms, bonds, and ribbons are opened as a VRML model with the same model number as the corresponding molecule model. These models can be closed or hidden with the Model Panel, or undisplayed/displayed (hidden/shown) with the command objdisplay.

• Separate glycosidic bond (true/false) - only relevant to tube / slab display; whether the tubes should include a segment along the glycosidic (sugar-base) bond. For slab styles that do not engulf this bond (long, skinny), this shows each tube as two segments, like an elbow. For slab styles that enclose this bond (big, fat) this changes the angle at which the tube connects to the slab.
• Thickness (default 0.5 Å) - slab thickness
• Slab object (box/elliptical tube/ellipsoid) - slab shape
• Hide base atoms (true/false) - whether to hide the atoms and bonds in bases when slabs are shown
• Slab style (big/fat/long/skinny) - sets slab dimensions and location relative to base atoms; new slab styles can be created and listed here using the Slab Style section

Parameters in this section collectively define a slab style, or slab dimensions and location relative to the atoms in purine and pyrimidine bases. Slab styles can be named, saved, and later retrieved from the pulldown list indicated by the solid black triangle. When the name of a built-in style (big, fat, long, or skinny) is shown, it is only possible to save to a different name, using Save As.... When another name is shown, it is possible to:

• Save the slab style to the name shown
• use Save As... to save the slab style to a new name
• Delete the slab style whose name is shown (if previously saved)

Purine and Pyrimidine slab style options include:

• Anchor - name of the atom in the base to be used as an anchor for the slab position
• Lower left - position of the slab's lower left corner (as shown in the adjacent cartoon) in angstroms from the anchor atom position; the first number is distance along the X-axis in the standard reference frame (positive means to the right) and the second is distance along the Y-axis in the standard reference frame (negative means downward)
• Upper right - position of the slab's upper right corner (as shown in the adjacent cartoon) in angstroms from the anchor atom position; the first number is distance along the X-axis in the standard reference frame (positive means to the right) and the second is distance along the the Y-axis in the standard reference frame (negative means downward)

The standard reference frame is described in:

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.

• Skip non-base H bonds (true/false) - whether to consider only base atoms when identifying H-bonds; otherwise, all nucleic acid atoms will be considered (default)
• Show stubs (true/false) - whether to show bases without H-bonds to other bases as half-rungs (default) or not at all
• Rung radius (default 0.45 Å) - radius to use for ladder rungs showing H-bonds between bases, and for stubs representing bases that lack H-bonds to other bases (a smaller radius is used to show H-bonds involving non-base atoms)
• Relax H-bond constraints (off by default) - whether to relax the strict geometric criteria for identifying H-bonds. The default relaxation amounts are 0.4 Å and 20.0°.

State not saved in sessions. Although sessions will include any VRML model created by Nucleotides, information such as which atoms were hidden by the nucleotide representations and which Nucleotides settings were used is not retained. After restarting a session, it is usually necessary to remake the Nucleotides model.

Some nonstandard residues not handled. Residues handled are A, DA, T, DT, C, DC, G, DG, U, PSU (pseudouridine base), and I (inosine base), as well as certain modified versions:

• described in MODRES records
• in which the base ring atoms are unchanged (for example, methylated or brominated derivatives)