/* Interesting test proteins */

andreasprlic · andreasprlic · commit c0a3daaeea44 · 2016-03-18T23:28:42.000-07:00
diff --git a/wiki/BioJava:CookBook:PDB:align.md b/wiki/BioJava:CookBook:PDB:align.md
@@ -62,11 +62,14 @@ javadoc.
     setting the *Maximum Gap Size* parameter in CE to *unlimited* (-1)
     allows it to find the whole barrel.
     ([Example](http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_ce&mol=1tim.A&mol=1cdg.A) -
-    default gap size)
-
-<!-- -->
-
-1.  4hhb.A vs. 4hhb.B See how the visualisation tools in BioJava can
+    CE with default gap size)
+2.  4hhb.A vs. 4hhb.B See how the visualisation tools in BioJava can
     also display a superposition of the **ligands** in an alignment.
     ([Example](http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_ce&mol=4hhb.A&mol=4hhb.B))
+3.  1a64.A vs. 1hng.B . Domain swapping. In this example the similarity
+    between the two chains can best be found using the FATCAT-flexible
+    algorithm (Compare these examples:
+    [FATCAT-flexible](http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_fatcat_flexible&mol=1hng.B&mol=1a64.A)
+    vs.
+    [CE](http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_ce&mol=1HNG.B&mol=1A64.A)
 
diff --git a/wiki/BioJava:CookBook:PDB:align.mediawiki b/wiki/BioJava:CookBook:PDB:align.mediawiki
@@ -25,6 +25,6 @@ Also know as "overlaying" is a process of fitting two (equivalent) sets of Atoms
 
 === Interesting test proteins ===
 
-# 1cdg.A vs 1tim.A . A TIM barrel aligned with a '''multi domain protein''' that contains a TIM barrel. While default CE and FATCAT (rigid) parameters only manage to find 3/4 of the barrel aligned, setting the ''Maximum Gap Size'' parameter in CE to ''unlimited'' (-1) allows it to find the whole barrel. ([http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_ce&mol=1tim.A&mol=1cdg.A Example] - default gap size)
-
-# 4hhb.A vs. 4hhb.B See how the visualisation tools in BioJava can also display a superposition of the '''ligands''' in an alignment. ([http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_ce&mol=4hhb.A&mol=4hhb.B Example])
+# 1cdg.A vs 1tim.A . A TIM barrel aligned with a '''multi domain protein''' that contains a TIM barrel. While default CE and FATCAT (rigid) parameters only manage to find 3/4 of the barrel aligned, setting the ''Maximum Gap Size'' parameter in CE to ''unlimited'' (-1) allows it to find the whole barrel. ([http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_ce&mol=1tim.A&mol=1cdg.A Example] - CE with default gap size)
+# 4hhb.A vs. 4hhb.B See how the visualisation tools in BioJava can also display a superposition of the '''ligands''' in an alignment. ([http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_ce&mol=4hhb.A&mol=4hhb.B Example])
+# 1a64.A vs. 1hng.B . Domain swapping. In this example the similarity between the two chains can best be found using the FATCAT-flexible algorithm (Compare these examples: [http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_fatcat_flexible&mol=1hng.B&mol=1a64.A FATCAT-flexible] vs. [http://www.rcsb.org/pdb/workbench/workbench.do?action=pw_ce&mol=1HNG.B&mol=1A64.A CE]
