A pseudobond is drawn between two atoms to signify a connection other than a covalent bond, such as a hydrogen bond, metal coordination bond, or missing peptide segment. A pseudobond model is a named set of pseudobonds that can be treated collectively. Pseudobonds can be defined arbitrarily by creating and opening a pseudobond file. See also: hbonds, clashes/contacts, distance, struts
A pseudobond is only shown when both of its endpoint atoms are shown. Since a backbone atom is considered as shown when only its cartoon is shown, a pseudobond (which goes the atom position) may appear to be floating in space. Floating pseudobonds in the presence of cartoon can be hidden with the command cartoon suppress false, which also enables explicitly showing any backbone atoms of interest (at the same time as the cartoon). See also: display hierarchy
Commands that act on pseudobonds in general include color, style, size, label, show, hide, close, and crosslinks. For example, an interactive histogram of pseudobond lengths can be plotted with crosslinks histogram. Pseudobonds can also be selected by length. Pseudobonds can be specified in commands by their endpoint atoms, pseudobond model number, or built-in classifications: sel (when selected), pbonds, hbonds.