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.

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

• 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. Sugar pucker is evaluated when filled-ring representations are generated, and ribose ring atoms outside the plane are assigned an attribute named pucker with values of endo (same side as C5') or exo (opposite C5').
• 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 viewing coordinate system (positive means to the right) and the second is distance along the the Y-axis in the viewing coordinate system (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 viewing coordinate system (positive means to the right) and the second is distance along the the Y-axis in the viewing coordinate system (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.