X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhelp.jhm;h=5fb79011a498d765c32506aa0d313b618f59fdfb;hb=HEAD;hp=0c39a52a7509b1c3281a588819293160559ddef3;hpb=590fbc1d8dd620511a02a77596631764219c370c;p=jalview.git

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 0c39a52..5fb7901 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -65,10 +65,10 @@
    <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="clarguments-intro" url="html/features/clarguments-intro.html"/>
    <mapID target="clarguments-basic" url="html/features/clarguments-basic.html"/>
    <mapID target="clarguments-advanced" url="html/features/clarguments-advanced.html"/>
    <mapID target="clarguments-argfiles" url="html/features/clarguments-argfiles.html"/>
+   <mapID target="clarguments-reference" url="html/features/clarguments-reference.html"/>
    <mapID target="clarguments-old" url="html/features/clarguments-old.html"/>
    <mapID target="jvlfiles" url="html/features/jvlfiles.html"/>
    <mapID target="io" url="html/io/index.html"/>
@@ -161,7 +161,10 @@
    <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="structureandpaefromfile" url="html/features/structurechooser.html#loadfromfile" />
    <mapID target="structuresvia3dbeacons" url="html/features/structurechooser.html#3dbeaconssearch" />   
+   <mapID target="workingwithpae" url="html/features/paematrices.html" />
+   <mapID target="paematrixformat" url="html/io/paematrixformat.html" />
    <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
    <mapID target="biojsmsa" url="html/features/biojsmsa.html" />