/* Interesting test proteins */

andreasprlic · andreasprlic · commit 440df1a7d1cf · 2016-03-18T23:28:42.000-07:00
diff --git a/wiki/BioJava:CookBook:PDB:align.md b/wiki/BioJava:CookBook:PDB:align.md
@@ -55,3 +55,18 @@ tool for this. (See the
 javadoc.
 
 ### Interesting test proteins
+
+1.  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.
+    ([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
+    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))
+
diff --git a/wiki/BioJava:CookBook:PDB:align.mediawiki b/wiki/BioJava:CookBook:PDB:align.mediawiki
@@ -23,4 +23,8 @@ BioJava 1.7 contains an unpublished structure alignment algorithm. For more info
 
 Also know as "overlaying" is a process of fitting two (equivalent) sets of Atoms onto each other. This can be useful e.g. to overlay two different structural models of the same protein. BioJava also provides a tool for this. (See the [http://www.biojava.org/docs/api/org/biojava/bio/structure/SVDSuperimposer.html SVDSuperimposer.html] javadoc.
 
-=== Interesting test proteins ===
+=== 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])
