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JAL-1528 found and readded Colour by Chain ('rainbow color')
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 21 Nov 2014 14:33:08 +0000
(14:33 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 21 Nov 2014 14:33:08 +0000
(14:33 +0000)
help/html/features/chimera.html
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resources/lang/Messages.properties
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src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
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src/jalview/gui/ChimeraViewFrame.java
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diff --git
a/help/html/features/chimera.html
b/help/html/features/chimera.html
index
e866597
..
236701a
100644
(file)
--- a/
help/html/features/chimera.html
+++ b/
help/html/features/chimera.html
@@
-133,6
+133,8
@@
atoms in the displayed structures. For comprehensive details of Chimera's comman
they are insertions (relative to the associated sequence in the
alignment) and grey if they are N or C terminal flanks outside the
region mapped to the alignment window's sequence.</em></li>
they are insertions (relative to the associated sequence in the
alignment) and grey if they are N or C terminal flanks outside the
region mapped to the alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em>Uses the Chimera 'rainbow chain' command to apply a different colour to each chain.</em></li>
<li><strong>Charge & Cysteine<br>
</strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
<li><strong>Charge & Cysteine<br>
</strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
diff --git
a/resources/lang/Messages.properties
b/resources/lang/Messages.properties
index
5d3667b
..
cabee76
100644
(file)
--- a/
resources/lang/Messages.properties
+++ b/
resources/lang/Messages.properties
@@
-107,7
+107,7
@@
action.change_params = Change Parameters
action.apply = Apply
action.apply_threshold_all_groups = Apply threshold to all groups
action.apply_all_groups = Apply to all Groups
action.apply = Apply
action.apply_threshold_all_groups = Apply threshold to all groups
action.apply_all_groups = Apply to all Groups
-action.by_chain = By chain
+action.by_chain = By Chain
action.by_sequence = By Sequence
action.paste_annotations = Paste Annotations
action.format = Format
action.by_sequence = By Sequence
action.paste_annotations = Paste Annotations
action.format = Format
diff --git
a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index
090b61d
..
fb03f04
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@
-343,8
+343,7
@@
public abstract class JalviewChimeraBinding extends
public void colourByChain()
{
colourBySequence = false;
public void colourByChain()
{
colourBySequence = false;
- // this is not a valid Chimera command; is there one? Menu option hidden
- evalStateCommand("select *;color chain",false);
+ evalStateCommand("rainbow chain", false);
}
public void colourByCharge()
}
public void colourByCharge()
diff --git
a/src/jalview/gui/ChimeraViewFrame.java
b/src/jalview/gui/ChimeraViewFrame.java
index
cfac4ef
..
02865e1
100644
(file)
--- a/
src/jalview/gui/ChimeraViewFrame.java
+++ b/
src/jalview/gui/ChimeraViewFrame.java
@@
-144,9
+144,6
@@
public class ChimeraViewFrame extends GStructureViewer implements Runnable,
_alignwith = new Vector<AlignmentPanel>();
}
_alignwith = new Vector<AlignmentPanel>();
}
- // no colour by chain command in Chimera?
- chainColour.setVisible(false);
-
// save As not yet implemented
savemenu.setVisible(false);
// save As not yet implemented
savemenu.setVisible(false);