nucleotide displays

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. Nucleotides representations are included in saved sessions. See also: fillring and the following reference:

Nucleic acid visualization with UCSF Chimera. Couch GS, Hendrix DK, Ferrin TE. Nucleic Acids Res. 2006 Feb 14;34(4):e29.
There are several ways to start Nucleotides, a tool in the Depiction category. It can be called from the Atoms/Bonds section of the Actions menu. It is also implemented as the command nucleotides. Options:

Clicking NDB Colors sets atom and ribbon colors according to the convention used in the Nucleic Acid Database (NDB): A red, T blue, C yellow, G green, and U cyan.

Special nucleotide representations will be created only where the corresponding atoms are displayed, and will be colored to match the atoms. 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.

Slab Options

Slab Style

A slab style refers to the slab dimensions and location relative to the atoms in purine and pyrimidine bases. The settings define a virtual rectangle in the plane of the base, as shown in the schematic diagrams in the dialog. Ellipsoid slab objects will be drawn to enclose the the virtual rectangle. Changes in Slab Style settings will be shown in the schematics, but will not affect the Chimera display until either Apply or OK is clicked.

The built-in slab styles are big, fat, long (default), and skinny. 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 is shown, it is only possible to save to a different name, using Save As.... When another name is shown, it is possible to:

Custom slab styles are saved in the Chimera preferences file, and are only updated with any changes when Save, Save As... or Delete is used.

The Anchor is the point of reference for the virtual rectangle:

Purine and Pyrimidine settings each include: 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.

Ladder Options


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:

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 / September 2010