Difference between revisions of "Valence"

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(added information to the valence command and distinguished it from the settings along with minor edits)
 
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== Overview ==
 
== Overview ==
Turning on '''valence''' will force PyMol to show double bonds as double lines -- instead of the normal view, as when it's turned off.
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Turning on the '''valence''' setting will enable the display of double bonds.<br>
 
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Toggling '''valence_mode''' alters the positioning of double bonds (for representation as [[Lines]])<br>
 
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'''valence_size''' alters the distance of double bonds.<br>
== Examples ==
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Note that bonds can be edited to be delocalized using [[Unbond]] and [[Bond]].<br>
[[Image:Valence0.png|left|thumb|Valence off]]
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There is also a command called '''valence'''.<br>
[[Image:Valence1.png|left|thumb|Valence on]]
 
  
  
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== Examples for the settings: valence and valence_mode ==
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<gallery heights="200px" widths="200px" align="left" perrow="4">
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Image:PHE_valence_0.png|set valence, 0<br>#(no double bonds)
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Image:PHE_valence_1_mode_1.png|set valence, 1<br>set valence_mode, 1<br>#bonds inside
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Image:PHE_valence_1_mode_0.png|set valence, 1<br>set valence_mode, 0<br>#bonds centered
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Image:PHE_delocalized.png|set valence, 1<br>#delocalized bonds<br>#(edited: see [[Bond]])
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</gallery>
  
  
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'''valence_size''' alters the distance of double bonds, but behaves slightly different depending on valence_mode<br>
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{| width="45%"
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|+ style="font-weight:bold; text-align:center; font-size:100%;" | valence_size
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! valence_size with valence_mode 1<br> inside !! valence_size with valence_mode 0 <br> centered
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|-
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||[[File:valence_size_mode1.gif]] ||  [[File:valence_size_mode0.gif]]
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|}
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=== Syntax ===
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<source lang="python">
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set valence, 0 # off
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set valence, 1 # on
  
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set valence_mode, 0 # centered
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set valence_mode, 1 # inside
  
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set valence_size, 0.1 # default: 0.06 # range 0 - ~0.5
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</source>
  
  
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== The valence command ==
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The '''valence''' command automatically formats existing bonds and can even guess the bonds for standard amino acids.<br>
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<source lang="python">
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#USAGE:
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valence order, selection1 [, selection2 [, source [, target_state [, source_state [, reset [, quiet ]]]]]]
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order can be either: 1, 2, 3, 4, aromatic, copy, guess
  
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#make PyMOL guess/autoformat bonds in proteins
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valence guess, all
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</source>
  
  
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== Editing bonds ==
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<source lang="python">
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# In editing mode: select the bond using Ctrl-right-click, then enter:
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unbond pk1,pk2
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bond pk1,pk2,4
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# 1: single bond, 2: double bond, 3:triple bond, 4:delocalized
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</source>
  
  
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==Automatic editing of bonds==
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Try using the '''valence''' command first.<br>
 +
Secondly, [[Format_bonds]] is a script that automatically formats valence in all amino acids and has additional options.
  
  
 +
==SEE ALSO==
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[[Bond]], [[Unbond]]
  
== Syntax ==
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[[Category:Settings|Valence]]
<source lang="python">
 
set valence, 0 # off
 
set valence, 1 # on
 
</source>
 

Latest revision as of 06:01, 22 April 2015

Overview

Turning on the valence setting 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.
There is also a command called valence.


Examples for the settings: valence and valence_mode


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


The valence command

The valence command automatically formats existing bonds and can even guess the bonds for standard amino acids.

#USAGE:
valence order, selection1 [, selection2 [, source [, target_state [, source_state [, reset [, quiet ]]]]]]
order can be either: 1, 2, 3, 4, aromatic, copy, guess

#make PyMOL guess/autoformat bonds in proteins
valence guess, all


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

Try using the valence command first.
Secondly, Format_bonds is a script that automatically formats valence in all amino acids and has additional options.


SEE ALSO

Bond, Unbond