Pseudobond Attributes

Once a group of pseudobonds has been chosen in the left side of the PseudoBond Panel, clicking the attributes... button in the right side of the panel brings up a window that shows and allows changes in pseudobond attribute values.

The list includes the attributes of the pseudobond group and selected attributes of its component pseudobonds. A chain trace is a special case of a pseudobond group. Descriptions in the dialog are not necessarily identical to the attribute names (used in the code and in various commands).

PseudoBondGroup Attributes

• category - name of the pseudobond group
• color (a color well) - color at the pseudobond group level; see coloring hierarchy
• changing group color removes individual colors - whether changing the group-level color (above) will change all pseudobonds in the group to that color and erase memory of any individually assigned colors (individually assigned colors override the group-level color; see coloring hierarchy)
  • false
  • true
• displayed - whether display is enabled at the pseudobond group level (see display hierarchy)
  • false
  • true
• line style - how to show pseudobonds in the wire draw mode:
  • –––
  • – –
  • ·  ·
  • – ·
  • – ··
• line width - pixel width of pseudobonds in the wire draw mode
• stick scale - scale factor for pseudobonds in the stick draw mode. The stick scale is multiplied by individual pseudobond radii (default 0.2 angstroms) to generate stick radii in angstroms.

ChainTrace Attributes

A chain trace is a special case of a pseudobond group; it has the same attributes (listed above) as a generic group, plus:

• track molecule - whether the chain trace attributes should change accordingly when certain attributes of the associated molecule model are changed (dashed line enabling, dash characteristics, line width, stick scale, component bond style and halfbond mode)
  • false
  • true

Component PseudoBond Attributes

Attributes of individual pseudobonds within a pseudobond group can be set independently. When different pseudobonds within the group have different attribute values, the value is reported to be -- multiple --. If one of the other options is chosen, all pseudobonds in the group will be changed accordingly.

• bond style - pseudobond draw mode
  • -- multiple --
  • wire
  • stick
  • spring
• color (a color well) - color at the individual pseudobond level; see coloring hierarchy. Note that the color assigned to the pseudobond will only be visible when halfbond mode is off; when halfbond mode is on, pseudobond color comes from the flanking atoms.
• displayed - whether display is enabled at the individual pseudobond level (see display hierarchy)
  • -- multiple --
  • true
  • false
  • if atoms shown (dependent on the display of the flanking atoms; when halfbond mode is on, each half will be displayed if the corresponding atom is displayed; when halfbond mode is off, the pseudobond will be displayed only when both atoms are displayed)
• halfbond mode - whether the two halves of a pseudobond are handled as separate entities; when halfbond mode is on, the color of each halfbond matches that of the attached atom (except if the bond style is spring, one atom's color is used for the whole pseudobond)
  • -- multiple --
  • on
  • off
• label - text label for the pseudobond; if the pseudobond is a distance monitor, this label reports the distance. Label text can also be assigned when a pseudobond is created with PseudoBond Reader.
• label color (a color well) - if a label has no color of its own, it will inherit the color of its associated pseudobond; see coloring hierarchy
• radius - value to be multiplied by the pseudobond group stick scale to generate stick radius in angstroms (only applies to pseudobonds in the stick draw mode)