X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmol.java;fp=src%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmol.java;h=cb197693e1a34cf1bb50d60f7abda52faf057c47;hb=1fcd6eb366ba3d4c1a0f41c881ad6f6357be240f;hp=240ea7bc00b4df37bbe05cb157360fcbf1123945;hpb=c2998dd409165095887a3aec405837ecbb3b4ffe;p=jalview.git

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 240ea7b..cb19769 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -242,6 +242,19 @@ public class PDBFileWithJmol extends AlignFile implements
                 lastrnum = group.getResno();
               }
               seq[len] = group.getGroup1();
+
+              /*
+               * JAL-1828 replace a modified amino acid with its standard
+               * equivalent (e.g. MSE with MET->M) to maximise sequence matching
+               */
+              String threeLetterCode = group.getGroup3();
+              String canonical = ResidueProperties.getCanonicalAminoAcid(threeLetterCode);
+              if (canonical != null
+                      && !canonical.equalsIgnoreCase(threeLetterCode))
+              {
+                seq[len] = ResidueProperties
+                        .getSingleCharacterCode(canonical);
+              }
               switch (group.getProteinStructureSubType())
               {
               case HELIX310: