update to 1.8

Gwaldon · andreasprlic · commit 995041b85406 · 2016-03-18T23:29:01.000-07:00
diff --git a/wiki/BioJava:CookBookLegacy.md b/wiki/BioJava:CookBookLegacy.md
@@ -263,29 +263,8 @@ How Do I....?
 
 ### Protein Structure
 
--   [How can I parse a PDB file?](BioJava:CookBook:PDB:read "wikilink")
--   [How can I parse a .mmcif
-    file?](BioJava:CookBook:PDB:mmcif "wikilink")
--   [How can I access the atoms in a
-    structure?](BioJava:CookBook:PDB:atoms "wikilink")
--   [How can I do calculations on
-    atoms?](BioJava:CookBook:PDB:atomsCalc "wikilink")
--   [How to work with Groups (AminoAcid, Nucleotide,
-    Hetatom)?](BioJava:CookBook:PDB:groups "wikilink")
--   [How can I access the header information of a PDB
-    file?](BioJava:CookBook:PDB:header "wikilink")
--   [How does BioJava deal with SEQRES and ATOM
-    groups?](BioJava:CookBook:PDB:seqres "wikilink")
--   [How can I mutate a
-    residue?](BioJava:CookBook:PDB:mutate "wikilink")
--   [How can I calculate a structure
-    alignment?](BioJava:CookBook:PDB:align "wikilink")
--   [How can I use a simple GUI to calculate an
-    alignment?](BioJava:CookBook:PDB:alignGUI "wikilink")
--   [How can I interact with
-    Jmol?](BioJava:CookBook:PDB:Jmol "wikilink")
--   [How can I serialize to a
-    database?](BioJava:CookBook:PDB:hibernate "wikilink")
+Since BioJava 1.8, all protein structure modules have moved to
+[BioJava3](BioJava:CookBook "wikilink").
 
 ### Ontologies
 
diff --git a/wiki/BioJava:CookBookLegacy.mediawiki b/wiki/BioJava:CookBookLegacy.mediawiki
@@ -150,18 +150,7 @@ And lets not forget this new [[BioJava:CookBookItaliano|Italian]] translation (t
 
 === Protein Structure ===
 
-* [[BioJava:CookBook:PDB:read|How can I parse a PDB file?]]
-* [[BioJava:CookBook:PDB:mmcif|How can I parse a .mmcif file?]]
-* [[BioJava:CookBook:PDB:atoms|How can I access the atoms in a structure?]]
-* [[BioJava:CookBook:PDB:atomsCalc|How can I do calculations on atoms?]]
-* [[BioJava:CookBook:PDB:groups|How to work with Groups (AminoAcid, Nucleotide, Hetatom)?]]
-* [[BioJava:CookBook:PDB:header|How can I access the header information of a PDB file?]]
-* [[BioJava:CookBook:PDB:seqres|How does BioJava deal with SEQRES and ATOM groups?]]
-* [[BioJava:CookBook:PDB:mutate|How can I mutate a residue?]]
-* [[BioJava:CookBook:PDB:align|How can I calculate a structure alignment?]]
-* [[BioJava:CookBook:PDB:alignGUI|How can I use a simple GUI to calculate an alignment?]]
-* [[BioJava:CookBook:PDB:Jmol|How can I interact with Jmol?]]
-* [[BioJava:CookBook:PDB:hibernate|How can I serialize to a database?]]
+Since BioJava 1.8, all protein structure modules have moved to [[BioJava:CookBook|BioJava3]].
 
 === Ontologies ===
 * [[BioJava:CookBook:OBO:parse|How can I parse an OBO file?]]
