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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, and a chain network diagram summarizing intra- and interchain pseudobonds can be shown with crosslinks network. 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:

Example pseudobond file contents:

; open this example pb file after commands: open 1bna; color tan targ f
; halfbond = true
; color = magenta
; radius = 0.1
; dashes = 12
/a:1@c3' /a:1@n3
/a:2@c3' /a:2@n1
/a:3@c3' /a:3@n3
/a:4@c3' /a:4@n1
/a:5@c3' /a:5@n1
/a:6@c3' /a:6@n1
/a:7@c3' /a:7@n3
/a:8@c3' /a:8@n3
/a:9@c3' /a:9@n3
/a:10@c3' /a:10@n1
/a:11@c3' /a:11@n3
/a:12@c3' /a:12@n1
; halfbond = false
; color = 0,100,0,50
; radius = 0.2
; dashes = 4
/b:13@c3' /b:13@n3
/b:14@c3' /b:14@n1
/b:15@c3' /b:15@n3 red
/b:16@c3' /b:16@n1
/b:17@c3' /b:17@n1
/b:18@c3' /b:18@n1 dodgerblue
/b:19@c3' /b:19@n3
/b:20@c3' /b:20@n3
/b:21@c3' /b:21@n3
/b:22@c3' /b:22@n1
/b:23@c3' /b:23@n3 80,50,0
/b:24@c3' /b:24@n1

In this example, no pseudobonds will be shown as magenta because their halfbond setting is true; instead, each half will be colored to match the atom on that side. All of the pseudobonds will have 4 dashes because only one dashes setting is applied per file. (Different pseudobond files are needed to define sets of pseudobonds with different numbers of dashes.)

UCSF Resource for Biocomputing, Visualization, and Informatics / March 2020