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=240ea7bc00b4df37bbe05cb157360fcbf1123945;hb=f06554784411ddbf871d642e66c8dcb7f147d4a8;hp=3b6f0c221b864a83778019994a253984633b47c3;hpb=cf06ee5d732af6cc874115aece1138adafca8ad7;p=jalview.git

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 3b6f0c2..240ea7b 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -176,8 +176,14 @@ public class PDBFileWithJmol extends AlignFile implements
                   newseq[p] = cinds[seq[p]] == nonGap ? ngc : seq[p];
                   if (secstr[p] >= 'A' && secstr[p] <= 'z')
                   {
-                    asecstr[p] = new Annotation("" + secstr[p], null,
-                            secstrcode[p], Float.NaN);
+                    try
+                    {
+                      asecstr[p] = new Annotation("" + secstr[p], null,
+                              secstrcode[p], Float.NaN);
+                    } catch (ArrayIndexOutOfBoundsException e)
+                    {
+                      // skip - patch for JAL-1836
+                    }
                   }
                 }
                 String modelTitle = (String) ms