Difference between revisions of "Valence"

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=SEE ALSO=
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==Automatic editing of bonds==
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[[Format_bonds]] is a script that automatically formats valence in amino acids.
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==SEE ALSO==
 
[[Bond]], [[Unbond]]
 
[[Bond]], [[Unbond]]
  
 
[[Category:Settings|Valence]]
 
[[Category:Settings|Valence]]

Revision as of 16:42, 9 June 2014

Overview

Turning on valence 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.


Examples


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

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


Syntax

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 

# 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

Format_bonds is a script that automatically formats valence in amino acids.


SEE ALSO

Bond, Unbond