X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhelp%2Fhelp.jhm;h=1710bbc764d00e94766a9139f8430e6a977b01fa;hb=49e67ec82b0557edb2b4c660fb61913fa453c651;hp=aecd1a4720f28bdb1fa90885d65c25862d2a67f6;hpb=5adb410f9f92defbfe2ec572584c2f6f4d133022;p=jalview.git

diff --git a/help/help/help.jhm b/help/help/help.jhm
index aecd1a4..1710bbc 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -47,6 +47,7 @@
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
    <mapID target="seqfeatedit" url="html/features/editingFeatures.html"/>
    <mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>
+   <mapID target="seqfeatures.report" url="html/features/seqfeaturereport.html"/>
    <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
    <mapID target="seqfeatures.settings.selcols" url="html/features/featuresettings.html#selectbyfeature"/>
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
@@ -54,12 +55,15 @@
    <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
    <mapID target="pdbjmol" url="html/features/jmol.html"/>
    <mapID target="chimera" url="html/features/chimera.html"/>
+   <mapID target="pymol" url="html/features/pymol.html"/>
    <mapID target="chimera.annotxfer" url="html/features/chimera.html#annotxfer"/>
    <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"/>
@@ -91,6 +95,10 @@
    <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" />
@@ -147,6 +155,7 @@
    <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" />
    
@@ -169,4 +178,5 @@
    
    <mapID target="importvcf" url="html/features/importvcf.html" />
    <mapID target="importvcf.attribs" url="html/features/importvcf.html#attribs" />
+   <mapID target="logging" url="html/logging.html" />
 </map>