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Revision as of 05:01, 22 April 2015 by Andwar (talk | contribs) (added information to the valence command and distinguished it from the settings along with minor edits)
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Turning on the valence setting 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.
There is also a command called valence.

Examples for the settings: valence and valence_mode

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

valence_size with valence_mode 1
valence_size with valence_mode 0
Valence size mode1.gif Valence size mode0.gif


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

The valence command

The valence command automatically formats existing bonds and can even guess the bonds for standard amino acids.

valence order, selection1 [, selection2 [, source [, target_state [, source_state [, reset [, quiet ]]]]]]
order can be either: 1, 2, 3, 4, aromatic, copy, guess

#make PyMOL guess/autoformat bonds in proteins
valence guess, all

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

Try using the valence command first.
Secondly, Format_bonds is a script that automatically formats valence in all amino acids and has additional options.


Bond, Unbond