The Display menu contains a series of check boxes which determine which
types of objects are to be displayed. Only the selected items will be
drawn in the graphics window. This provides a means of turning on or off
an entire class of objects at a time. This is distinct from ``hiding''
objects by coloring them with color 0, in that when an object is not
selected in this menu, it will not be drawn regardless of its color. The
initial state of this menu is taken from the .spockrc initialization
file (§3.8); its contents are saved with the ``Save
Preferences'' menu option (§6.1.2). The different
classes of objects are detailed below. For many objects, more details are
given in §6.4.
If selected, bonds of the type
specified by the ``Alter Bonds'' menu (§6.4.1) are drawn
between atoms. Atoms with no bonds (metal atoms, water) are represented
with a simple cross.
If selected, dashed lines will be drawn between those atoms which are
hydrogen bonded. All H-bonds are the same color (color 51 by default, but
this may be changed via the hbc=n command) and H-bonds are only
drawn for those atoms which are not colored 0 at the time ``Display
H-Bonds'' is selected. For information on how to specify H-Bonds see §
6.7.10 and 6.7.13. Some
PDB files specify H-bonds, and spock will use this information.
If selected, Atoms of the type
specified by the ``Alter Atoms'' menu (§6.4.2) are drawn
If selected, a backbone ribbon or
``worm'' of the type specified by the ``Alter Worms'' menu (§
6.4.3). A worm is built by default through both the alpha
carbon backbone of proteins and the phosphorus atoms of nucleic acids.
If selected, spock draws a line or cylinder connecting adjacent
-carbon atoms. In order to save memory, spock does not have full
control over the CA trace as it does for bonds or atoms. Instead the
coloring options for the CA trace are 1) a single color for all CA traces
(via e.g. cac=2) 2) color each molecule's CA trace a different color
(via cac=n) 3) color the CA trace by atom color (via
cac=a[tom]) 4) color the CA trace by bond color (via the
If selected, spock will draw
any surfaces as defined by the ``Alter Surfaces'' menu (§
calculates surface areas (via the Calculate surface area menu §
6.6.3) the surface points generated are saved in a
display list. Toggling this option on displays the points. This is quite
distinct from the surfaces option above.
This option will draw a plane parallel to the screen, showing 2D contours
currently defined. The position of this plane along the screen Z axis
(into and out of the screen) may be changed via the Clipping Tool §
spock will draw any isopotential contours defined by the ``Alter
Contours'' menu (§6.4.6).
Spock can read,
contour, and display XPLOR-format electron density maps. The contouring
algorithm is slightly different from the 3D contours above, which is why
there is a separate option for electron density maps. Electron density
maps may also be contoured using the same algorithm as the 3D contours, as
described for the ``Alter density maps'' menu §6.4.7.
This option toggles the drawing of a coordinate frame along the X (red), Y
(green), and Z (blue) axes of the structure. This frame is centered at
the center of rotation of the molecule, which may be changed with the
set center command (§5.2.3), or via the Graphics
menu (§6.11). A set of 3-D arrows with the same color scheme
is also shown at the origin of rotation. The length of these arrows
(exclusive of the arrow head) is 1.0 Ångstroms, so the size of these
arrows can be used as an internal ruler, and can give a sense of scale.
This option toggles display of
cylinders representing the axes of helices. See the section on the
``Alter Helices'' menu for details (§6.4.8).
This option toggles display of
cylinders representing the major axes of strands of beta sheets. See the
section on the ``Alter Sheets'' menu for details (§6.4.9).
If this option is selected, spock will display cylinders representing
Watson-Crick base pairs in DNA and RNA. The cylinders extend from the
midpoints of the surrounding phosphates on each backbone, so the last base
pair on each end of a molecule may not be drawn. Hydrogen bonding
information is necessary to determine the base pairing, so if there is no
H-bonding information, no cylinders will be displayed. H-bonds may be
calculated via the Modeling Find H-bonds menu option (§
6.7.10). Only perfect Watson-Crick base pairs are
found. If you wish cylinders between other base pairs, you may specify
the cylinders in an external objects file as described in Appendix
Note that the spokes are automatically updated whenever the hydrogen bond
information changes, such as after a H-Bond calculation, or deleting all
the hydrogen bonds (§6.7.10).
toggle display of all text labels and annotations, respectively. See the
section on the ``Alter Labels'' menu for details (§6.4.11).
If the crystal parameters are defined via the PDB file or via the Modeling
menu, toggling this on will display a wire-frame representation of the
unit cell. The color is always color 1 (white), unless the background is
white, in which case the unit cell is rendered in color 100 (black). A
set of 3-D arrows like those shown for the axis display is shown at
(0,0,0) in the atomic coordinate system (the origin of the unit cell).
This option toggles
display of interaction cylinders or lines. An interaction is simply a
connection between two atoms with an associated value, for instance a
distance interaction. See §6.4.12 for more details.
read and objects from an external Raster3D file or a spock objects file.
Spock object files are described in Appendix F.3.
Worms, surfaces and interactions are usually colored by their assigned
colors. However, they may also be colored with a spectrum of colors such
that the color is interpolated to represent the value of a given property.
This option controls display of an on-screen key to the color values,
which also serve as interactive controls for the interpolation.
Using the spectrum controls: In order to use the spectrum interactive
controls, you must first position the cursor on the appropriate part of
the spectrum, then press and hold the appropriate mouse buttons for
the desired function. The available functions are as follows:
Midpoint: There are white triangles on either side of the spectrum.
Pressing and holding the left mouse button on this triangle while moving
the mouse will control the position of the midpoint value used for the
color interpolation. Maximum, Minimum: Pressing and holding the
mouse button on the spectrum itself above or below the midpoint indicator
allows control of the maximum or minimum value respectively. Moving the
mouse with this button held down will increase or decrease the extrema,
according to the direction of movement. Movement. Just as with the
main graphics display, the left and middle mouse button control
translations of the spectrum. If these buttons are pressed and held while
the cursor is on the spectrum, moving the mouse will move the spectrum.
Scaling: Again following the main graphics display, the middle mouse
button is used to control the size of the spectrum. Moving the mouse with
the middle button held down will scale the spectrum.
Each of the parameters controlled by the spectrum may also be set by the
``Edit spectrum'' option of the Alter Spectra menu §
This option turns on the display of bones files if any are currently in
memory. Bones are used by crystallographers in the course of building a
model. If you don't know what a bones file is, you probably don't need
This option turns off display of all
Tue Sep 14 16:44:48 CDT 1999