“set_bond” changes per-bond settings for all bonds which exist between two selections of atoms.

set_bond name, value, selection1 [, selection2 ]

name = string: name of the setting

value = string: new value to use

selection1 = string: first set of atoms

selection2 = string: seconds set of atoms {default: (selection1)}

set_bond stick_transparency, 0.7, */n+c+ca+o 

The following per-bond settings are currently implemented. Others may seem to be recognized but will currently have no effect when set at the per-bond level.

• valence
• line_width
• line_color
• stick_radius
• stick_color
• stick_transparency

Note that if you attempt to use the “set” command with a per-bond setting over a selection of atoms, the setting change will appear to take, but no change will be observed.

cmd.set_bond | commands

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