Nucleotides Nucleotides icon

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).
There are several ways to start Nucleotides, a tool in the Depiction category.

Options for backbone display are: Options for sugar display are: Options for base display are: Show base orientation (true by default) means that the positive faces of bases will be indicated 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.

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.

Slab Options

Further options affecting slab representations of bases are: The standard reference frame is described in:
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:

After showing these modified bases as slabs, it may be necessary to undisplay extra base atoms that were not hidden automatically.

UCSF Computer Graphics Laboratory / March 2008