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).
There are several ways to start
Nucleotides, a tool in the Depiction category.
Options for backbone display are:
Options for sugar display are:
- 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
Options for base display are:
- atoms/bonds
- filled - VRML showing the rings as filled in
- slab (default) - VRML slabs; several
further options affect this type of display
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:
- 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.
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).
LIMITATIONS
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)
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