Difference between revisions of "Format bonds"

From PyMOLWiki
Jump to: navigation, search
(Created page with "{{Infobox script-repo |type = Python Module |filename = format_bonds.py |author = Andreas Warnecke |license = BSD-2-Clause }} The script '''format_bon...")
 
(created script page; linked in valence page)
 
Line 30: Line 30:
 
* Remember to correctly configure plugin import (see: [[Git intro]])
 
* Remember to correctly configure plugin import (see: [[Git intro]])
 
* '''format_bonds''' will introduce delocalized bonds by default or when ''bonds'' is larger than 2.<br>
 
* '''format_bonds''' will introduce delocalized bonds by default or when ''bonds'' is larger than 2.<br>
* Setting ''bonds=1'' will simply disable valence (globally)
+
* 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.<br>
 
* The ''selection'' argument is 'all' by default and can be used to restrict editing to selected residues.<br>
 
* Note that '''format_bonds''' will also format acidic residues, the C-terminus, arginine and nitro groups.
 
* 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
+
* Tip: press the TAB key after entering format_bonds to get argument suggestions
  
  

Latest revision as of 17:33, 9 June 2014

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

The script format_bonds will automatically format bonds in amino acids.

Usage

format_bonds [ selection [, bonds ]]

Examples

import format_bonds

frag PHE
format_bonds

format_bonds bonds=2


Notes

  • 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


SEE ALSO

Git intro, Valence, Modeling and Editing Structures