Valence - Revision history

Bell: 2 revisions

2015-07-09T21:08:21Z

2 revisions

Andwar: added information to the valence command and distinguished it from the settings along with minor edits

2015-04-22T10:01:32Z

added information to the valence command and distinguished it from the settings along with minor edits

Andwar at 20:42, 9 June 2014

2014-06-09T20:42:19Z

Bell: 5 revisions

2014-06-09T14:21:59Z

5 revisions

Andwar: repaired misspelled unbond link

2014-06-06T12:32:01Z

repaired misspelled unbond link

Andwar: minor typo corrections

2014-06-04T21:49:55Z

minor typo corrections

Andwar: added descriptions for valence_size

2014-06-04T21:45:21Z

added descriptions for valence_size

Andwar at 20:51, 29 May 2014

2014-05-29T20:51:50Z

Andwar at 20:49, 29 May 2014

2014-05-29T20:49:59Z

Bell: 3 revisions

2014-03-28T03:36:22Z

3 revisions

New page

== 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.

== Examples ==
<gallery>
Image:Valence0.png|Valence off
Image:Valence1.png|Valence on
</gallery>

== Syntax ==
<source lang="python">
set valence, 0 # off
set valence, 1 # on
</source>

[[Category:Settings|Valence]]

@@ Line 1: / Line 1: @@
 == Overview ==
-Turning on '''valence''' will enable the display of double bonds.<br>
+Turning on the '''valence''' setting will enable the display of double bonds.<br>
 Toggling '''valence_mode''' alters the positioning of double bonds (for representation as [[Lines]])<br>
 '''valence_size''' alters the distance of double bonds.<br>
 Note that bonds can be edited to be delocalized using [[Unbond]] and [[Bond]].<br>
-== Examples ==
+== Examples for the settings: valence and valence_mode ==
 <gallery heights="200px" widths="200px" align="left" perrow="4">
 Image:PHE_valence_0.png|set valence, 0<br>#(no double bonds)
@@ Line 22: / Line 23: @@
 ||[[File:valence_size_mode1.gif]] ||  [[File:valence_size_mode0.gif]]
 |}
+=== Syntax ===
 <source lang="python">
 set valence, 0 # off
@@ Line 32: / Line 31: @@
 set valence_mode, 1 # inside
 set valence_size, 0.1 # default: 0.06 # range 0 - ~0.5
-# Editing bonds:
+#make PyMOL guess/autoformat bonds in proteins
 # In editing mode: select the bond using Ctrl-right-click, then enter:
 unbond pk1,pk2
@@ Line 43: / Line 57: @@
 ==Automatic editing of bonds==
-[[Format_bonds]] is a script that automatically formats valence in amino acids.
+Try using the '''valence''' command first.<br>

@@ Line 42: / Line 42: @@
-=SEE ALSO=
+==Automatic editing of bonds==
 [[Bond]], [[Unbond]]
 [[Category:Settings|Valence]]

@@ Line 3: / Line 3: @@
 Toggling '''valence_mode''' alters the positioning of double bonds (for representation as [[Lines]])<br>
 '''valence_size''' alters the distance of double bonds.<br>
-Note that bonds can be edited to be delocalized using [[Unond]] and [[Bond]].<br>
+Note that bonds can be edited to be delocalized using [[Unbond]] and [[Bond]].<br>
@@ Line 43: / Line 43: @@
 =SEE ALSO=
-[[Bond]], [[Unond]]
+[[Bond]], [[Unbond]]
 [[Category:Settings|Valence]]

@@ Line 2: / Line 2: @@
 Turning on '''valence''' will enable the display of double bonds.<br>
 Toggling '''valence_mode''' alters the positioning of double bonds (for representation as [[Lines]])<br>
-'''valence_size''' alters the distance of double bonds
+'''valence_size''' alters the distance of double bonds.<br>
 Note that bonds can be edited to be delocalized using [[Unond]] and [[Bond]].<br>
@@ Line 18: / Line 18: @@
 {| width="45%"
 |+ style="font-weight:bold; text-align:center; font-size:100%;" | valence_size
-! valence_size with valence_mode 1 !! valence_size with valence_mode 0
+! valence_size with valence_mode 1<br> inside !! valence_size with valence_mode 0 <br> centered
 |-
 ||[[File:valence_size_mode1.gif]] ||  [[File:valence_size_mode0.gif]]

@@ Line 2: / Line 2: @@
 Turning on '''valence''' will enable the display of double bonds.<br>
 Toggling '''valence_mode''' alters the positioning of double bonds (for representation as [[Lines]])<br>
-Note that bonds can be edited to be delocalized using [[Unond]] and [[Bond]].
+'''valence_size''' alters the distance of double bonds
@@ Line 12: / Line 13: @@
 Image:PHE_delocalized.png|set valence, 1<br>#delocalized bonds<br>#(edited: see [[Bond]])
 </gallery>
 == Syntax ==
@@ Line 21: / Line 32: @@
 set valence_mode, 1 # inside
-# In editing mode:
+set valence_size, 0.1 # default: 0.06 # range 0 - ~0.5
-# select the bond using Ctrl-right-click, then enter:
 unbond pk1,pk2
 bond pk1,pk2,4

← Older revision	Revision as of 21:08, 9 July 2015
(No difference)

← Older revision	Revision as of 14:21, 9 June 2014
(No difference)

@@ Line 25: / Line 25: @@
 unbond pk1,pk2
 bond pk1,pk2,4
-# 1: single bond, 2: double bond, triple bond, 4:delocalized
+# 1: single bond, 2: double bond, 3:triple bond, 4:delocalized
 </source>