/* Interesting test proteins */

andreasprlic · andreasprlic · commit 230b58e2f463 · 2016-04-09T10:58:48.000-07:00
diff --git a/_wikis/BioJava:CookBook:PDB:align.md b/_wikis/BioJava:CookBook:PDB:align.md
@@ -78,4 +78,5 @@ Tool](http://www.rcsb.org/pdb/workbench/workbench.do).
     [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)
+4.  1stp.A vs. 1swg.D . Circular permutation
 
diff --git a/_wikis/BioJava:CookBook:PDB:align.mediawiki b/_wikis/BioJava:CookBook:PDB:align.mediawiki
@@ -31,4 +31,5 @@ The protein structure modules of BioJava3 are used on the RCSB PDB web site for
 
 # 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]
+# 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]
+# 1stp.A vs. 1swg.D . Circular permutation
