Main Page

Type	Python Module
Download	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

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com

News & Updates
Official Release	PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released on December 2, 2014.
New Plugin	PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
PyMOL Open-Source Fellowship	Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release	PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released on August 4, 2014.
Official Release	PyMOL, AxPyMOL, and JyMOL v1.7 have all been released today, January 14, 2014.
New Plugin	Bondpack is 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 residues, the ..→

A Random PyMOL-generated Cover. See Covers.