Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects

[jalview.git] / help / help / help.jhm

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 78eaa70..cd415ea 100755 (executable)
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -63,6 +63,7 @@
    <mapID target="startupprefs" url="html/features/preferences.html#startup"/>     
    <mapID target="strucprefs" url="html/features/preferences.html#structure"/>     
    <mapID target="commandline" url="html/features/commandline.html"/>
+   <mapID target="jalviewcltool" url="html/features/commandline.html#script"/>
    <mapID target="clarguments" url="html/features/clarguments.html"/>
    <mapID target="jvlfiles" url="html/features/jvlfiles.html"/>
    <mapID target="io" url="html/io/index.html"/>
@@ -94,12 +95,17 @@
    <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
    <mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
    <mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />
+   <mapID target="colours.gecos-flower" url="html/colourSchemes/gecos-flower.html" />
+   <mapID target="colours.gecos-blossom" url="html/colourSchemes/gecos-blossom.html" />
+   <mapID target="colours.gecos-sunset" url="html/colourSchemes/gecos-sunset.html" />
+   <mapID target="colours.gecos-ocean" url="html/colourSchemes/gecos-ocean.html" />
    <mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />
    <mapID target="colours.helix" url="html/colourSchemes/helix.html" />
    <mapID target="colours.strand" url="html/colourSchemes/strand.html" />
    <mapID target="colours.turn" url="html/colourSchemes/turn.html" />
    <mapID target="colours.buried" url="html/colourSchemes/buried.html" />
    <mapID target="colours.nucleotide" url="html/colourSchemes/nucleotide.html" />
+   <mapID target="colours.nucleotideambiguity" url="html/colourSchemes/nucleotideambiguity.html" />
    <mapID target="colours.blosum" url="html/colourSchemes/blosum.html" />
    <mapID target="colours.pid" url="html/colourSchemes/pid.html" />
    <mapID target="colours.user" url="html/colourSchemes/user.html"/>