The pbond command creates a pseudobond between atom1 and atom2. A single specifier (for example, sel) can be used if it specifies exactly two atoms. Pseudobonds can also be generated by creating and opening a pseudobond file. See also: distance, hbonds, clashes/contacts, measurements
The pseudobonds can be removed with the pbond delete or ~pbond command. If atom1 and atom2 are specified, the pseudobond between them will be removed. Otherwise, an entire pseudobond model can be deleted by giving its name. The default name of the pseudobond model for creation and removal is custom. Pseudobond models can also be removed with the close command.
global
Giving the global keyword indicates a pseudobond model at the top level, instead of a submodel of an atomic structure. If a pseudobond's endpoint atoms are in two different models, however, its model will always be global; conversely, a pseudobond model containing pseudobonds that exist only in specific frame(s) of a trajectory (pseudobonds added with currentCoordsetOnly true) cannot be global.
reveal true | false
Whether to display the endpoint atoms to ensure that the pseudobond is displayed. To avoid showing disconnected atoms, the entire residues containing those atoms will be shown, except that amino acid and nucleic acid residues are split into sidechain and backbone moieties separately displayed by this option. Displayed backbone atoms may still be invisible where cartoon is shown, unless their simultaneous display has been enabled with cartoon suppress false.
showDist true | false
Whether to label the pseudobond with the corresponding distance. The distance label will update automatically if the endpoint atoms are moved relative to one another. Label color, height, and font can be adjusted with the label command, which can also be used to add the labels later or to delete them. Label height can also be set beforehand in the Labels preferences. The number of decimal places and whether to show the Å symbol can be changed with distance style or set beforehand in the Distances preferences.
color color-spec
Color to use for the pseudobond (default slate gray). The color can be changed later with the color command.
radius r
Radius in Å to use for the pseudobond (default 0.075); can be changed later with size.
dashes N
Number of dashes to use for the pseudobond (default 6). Only whole numbers are accepted, with 0 indicating solid sticks. Currently, odd numbers are rounded down to give an even number of dashes. The number of dashes can be changed later with style.
name name
Name for the pseudobond model (default custom, also the default name for deletion). Using a new name creates a separate model that can be hidden/shown/closed independently. Names containing spaces must be enclosed in quotation marks.
currentCoordsetOnly true | false
This option applies only to pseudobonds in a trajectory and indicates whether the pseudobond should exist across all trajectory frames (false, default) or only the current one. If the option is true, the pseudobond will exist only in the trajectory frame that was shown when the pseudobond was created, and if the pseudobond is displayed, it will only appear when that frame is played. All of the pseudobonds in a single pseudobond model must be of the same type (associated with the whole trajectory vs. associated with a specific trajectory frame). A pseudobond model with trajectory-frame-specific pseudobonds cannot be global.