Valence

Overview

Turning on valence will enable the display of double bonds.
Toggling valence_mode alters the positioning of double bonds (for representation as Lines)
valence_size alters the distance of double bonds.
Note that bonds can be edited to be delocalized using Unbond and Bond.

Examples

• 

  set valence, 0
  #(no double bonds)

• 

  set valence, 1
  set valence_mode, 1
  #bonds inside

• 

  set valence, 1
  set valence_mode, 0
  #bonds centered

• 

  set valence, 1
  #delocalized bonds
  #(edited: see Bond)

valence_size alters the distance of double bonds, but behaves slightly different depending on valence_mode

valence_size

valence_size with valence_mode 1 inside	valence_size with valence_mode 0 centered

Syntax

set valence, 0 # off
set valence, 1 # on

set valence_mode, 0 # centered
set valence_mode, 1 # inside

set valence_size, 0.1 # default: 0.06 # range 0 - ~0.5 

# Editing bonds:
# In editing mode: select the bond using Ctrl-right-click, then enter:
unbond pk1,pk2
bond pk1,pk2,4
# 1: single bond, 2: double bond, 3:triple bond, 4:delocalized

Automatic editing of bonds

Format_bonds is a script that automatically formats valence in amino acids.

SEE ALSO

Bond, Unbond