X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhelp.jhm;h=cd415eaf2e338835d0ed4c27ba36117c3d81ca3e;hb=366c4eed3d8a0bee653f9d4c0f16eebb9ff3cbb6;hp=449f34c3912b8228635f99af4d234fb1bdd78ce2;hpb=cc7e689bec78376ed404e42ec8f425496bb435c0;p=jalview.git

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 449f34c..cd415ea 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -60,8 +60,10 @@
    <mapID target="varna" url="html/features/varna.html"/>
    <mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
+   <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"/>
@@ -93,12 +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"/>
@@ -149,6 +156,7 @@
    <mapID target="pdbfts" url="html/features/pdbsequencefetcher.html#pdbfts" />
    <mapID target="siftsmapping" url="html/features/siftsmapping.html" />
    <mapID target="pdbchooser" url="html/features/structurechooser.html" />
+   <mapID target="structuresvia3dbeacons" url="html/features/structurechooser.html#3dbeaconssearch" />   
    <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
    <mapID target="biojsmsa" url="html/features/biojsmsa.html" />