Display

  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.  

Bonds

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.  

H-Bonds

  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.  

Atoms

If selected, Atoms of the type specified by the ``Alter Atoms'' menu (§6.4.2) are drawn between atoms.  

Worms

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.  

CA-trace

  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 cac=b[ond]) color.  

Surfaces

If selected, spock will draw any surfaces as defined by the ``Alter Surfaces'' menu (§ 6.4.5).  

Surface area dots

When spock 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.  

2D Contours

    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 § 6.11.4.  

3D Contours

If selected, spock will draw any isopotential contours defined by the ``Alter Contours'' menu (§6.4.6).  

Density maps

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.  

Axes

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.  

Helices

This option toggles display of cylinders representing the axes of helices. See the section on the ``Alter Helices'' menu for details (§6.4.8).  

Sheets

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).  

DNA spokes

    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 F.3.

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).  

Labels and Annotations

These options toggle display of all text labels and annotations, respectively. See the section on the ``Alter Labels'' menu for details (§6.4.11).  

Unit cell

  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).  

Interactions

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.  

External objects

Spock can read and objects from an external Raster3D file or a spock objects file. Spock object files are described in Appendix F.3.  

Spectra

  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 § 6.4.13.  

Bones

  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!  

None

This option turns off display of all objects.