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Type	Python Module
Download	scripts/format_bonds.py
Author(s)	Andreas Warnecke
License	BSD-2-Clause
	This code has been put under version control in the project Pymol-script-repo

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News & Updates
Official Release	PyMOL, AxPyMOL, and JyMO v1.7 have all been released] today, January 14, 2014.
New Plugin	Bondpack is a a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin	MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce	PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
New Plugin	GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software	CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script	cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks	Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News	See Older News.

Did you know...

The script format_bonds will automatically format bonds in amino acids.

Usage

format_bonds [ selection [, bonds ]]

import format_bonds

frag PHE
format_bonds

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 ..→

A Random PyMOL-generated Cover. See Covers.