X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhelp.jhm;h=6b06d36f7e54098eda6c7d51ddcde68e4afe8266;hb=f07e07b4ab966a2f617a0f9b25ee9f94b92b5825;hp=99d010dcca0a0d8772db3112a65fc838c43e8e4e;hpb=2720003e4d3537f99f6c1643561cbdb3d0120d2d;p=jalview.git

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 99d010d..6b06d36 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -55,12 +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"/>
@@ -148,6 +151,7 @@
    <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" />
    
@@ -170,4 +174,5 @@
    
    <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>