Format bonds

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Revision as of 16:33, 9 June 2014 by Andwar (talk | contribs) (created script page; linked in valence page)
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Type Python Module
Author(s) Andreas Warnecke
License BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

The script format_bonds will automatically format bonds in amino acids.


format_bonds [ selection [, bonds ]]


import format_bonds

frag PHE

format_bonds bonds=2


  • Remember to correctly configure plugin import (see: Git intro)
  • format_bonds will introduce delocalized bonds by default or when bonds is larger than 2.
  • Setting bonds=1 will simply disable valence display (globally!)
  • The selection argument is 'all' by default and can be used to restrict editing to selected residues.
  • Note that format_bonds will also format acidic residues, the C-terminus, arginine and nitro groups.
  • Tip: press the TAB key after entering format_bonds to get argument suggestions


Git intro, Valence, Modeling and Editing Structures