Pseudobonds are lines drawn between atoms to signify connections other than standard bonds. PseudoBond Reader creates arbitrary pseudobonds by reading in a text file that lists the pairs of atoms to be connected. Alternatively, if only a few pseudobonds need to be created, they can be added interactively as distance monitors (the distance labels can be turned off).
There are several ways to start PseudoBond Reader, a tool in the Depiction category. Starting PseudoBond Reader brings up a dialog for opening a user-created file of pseudobond information. Each line in the file describes one pseudobond and is of the form:
atom1 atom2 [color [label_text]]where atom1 and atom2 are atom specifications narrow enough to identify single atoms. Square brackets enclose optional fields. Fields are separated by spaces, except that label_text can contain any number of spaces. If a label is desired, a color must also be specified. Colors can be specified by name or by Tk color code. Examples of suitable lines of input:
#0:1@ca #0:2@ca dodger blue this is "dodger blue"The label for the first pseudobond in the example is this is "dodger blue" and the label for the second is a Tk code (the other two do not have labels). The label will be the same color as the corresponding pseudobond; label font and size can be set in the Background preferences.
:3@n #2:4@o #55ff88 a Tk code
#0:279.a@n #1:133.b@n red
Pseudobonds generated with the same input file are placed into a single group. Pseudobond group name, line width, and default model numbers for the specified atoms can be supplied. If no group name is given, the pathname of the input file is used. A default model number is used only for lines of input in which it is not specified. Since groups can be treated collectively in terms of attributes, it may be convenient to generate different sets of pseudobonds with different input files (to yield distinct groups). If pseudobonds with the same group name already exist, the new pseudobonds can either be added to the group or used to replace its previous members (if clear group... is set to true).
Pseudobond group display and other attributes can be controlled with the PseudoBond Panel. The attributes of an individual pseudobond can be changed by selecting it and using the Selection Inspector.