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:

G.S. Couch, D.K. Hendrix, and T.E. Ferrin, "Nucleic acid visualization with UCSF Chimera" Nucleic Acids Res 34:e29 (2006).

• atoms/bonds (default)
• ribbon - uses the nucleic acid rotated residue class
• classic ribbon - uses the nucleic acid residue class

• atoms/bonds
• filled (default) - VRML showing the rings as filled in. When filled-ring representations are generated, ribose ring atoms are assigned an attribute named pucker. Possible values of pucker are:
  • 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.
• tube - VRML tubes connecting the bases to the backbone; depending on how the bases are shown, it may be helpful to undisplay the glycosidic bond

• atoms/bonds
• filled - VRML showing the rings as filled in
• slab (default) - VRML slabs; several further options affect this type of display

VRML representations are created for only nucleic acid residues with displayed atoms, and are colored based on the atom coloring. 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 changes the display and dismisses the dialog; Apply changes 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.

VRML models are given the same model number as the corresponding molecule. VRML models can be closed or hidden independently from the corresponding molecule models with the Model Panel, or undisplayed/displayed (hidden/shown) with the command objdisplay.

• Thickness (0.5 by default) - angstrom thickness
• Slab object (box/elliptical tube/ellipsoid) - slab shape
• Hide base atoms (true/false) - whether to hide the atoms and bonds in bases; to show them after they have been hidden, it is necessary to set this option to false or to use a base display option other than slab
• Slab style (big/fat/long/skinny/custom) - a slab style includes the values of several parameters. Only the custom style can be edited; the values defining the other styles are shown, but grayed out:
  • Show glycosidic bond (true/false) - whether to show the bond connecting sugar and base; to show glycosidic bonds after they have been hidden, it is necessary to set this option to true or to use a base display option other than slab
  • 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)
    Thus, a virtual rectangle in the plane of the base can be defined relative to the position of the anchor atom. For ellipsoid slabs, the maximum width and length match the virtual rectangle, but the corners are smoothed.

W.K. Olson, M. Bansal, S.K. Burley, R.E. Dickerson, M. Gerstein, S.C. Harvey, U. Heinemann, X.J. Lu, S. Neidle, Z. Shakked, H. Sklenar, M. Suzuki, C.S. Tung, E. Westhof, C. Wolberger, and H.M. Berman, "A Standard Reference Frame for the Description of Nucleic Acid Base-Pair Geometry" J Mol Biol 313:229 (2001).

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.

Many 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)