ChimeraX docs icon


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, markers and links

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.

Pseudobonds can be saved to and read from files.

Pseudobond Files

Pseudobond file format (.pb) is a simple plain-text format that lists pairs of atoms to connect with pseudobonds. Pseudobond files can be opened and saved using the File menu or the commands open and save, respectively.

In this format, the columns cannot contain spaces because they are separated by spaces. The first two columns (required) are atom specifiers, and the third column (optional) is a color specifier. Blank lines and comment lines starting with a semicolon (;) may also be included, with radius given in a special comment line as shown below. The radius applies to pseudobonds defined on subsequent lines until another radius line is encountered. Example:

; example pseudobond definitions
/c:10@ca /c:14@ca dodgerblue
; radius = 0.8
#1/a:1@ca #3/a:85@ca
/b:30@o /c:24@o #ff4500
; radius = 0.4
/D:31@CA    /B:71@CA    20,70,70

A pseudobond is created for each line that specifies exactly two atoms. Defaults: color yellow
, radius 0.5 Å, dashes 8.

UCSF Resource for Biocomputing, Visualization, and Informatics / March 2019