X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fmc_view%2FPDBfile.java;h=2a89e61431fa3e19f92c8ab637e68d2c12f2550d;hb=e8f870fb9e3ccb05b9c1c2163e01919d346ce9de;hp=24e0435e0220df992af4cf4cd96451d9fd90be87;hpb=d46c8cbd1a5282ede9a0a94471f23ca002cf7df6;p=jalview.git

diff --git a/src/mc_view/PDBfile.java b/src/mc_view/PDBfile.java
index 24e0435..2a89e61 100755
--- a/src/mc_view/PDBfile.java
+++ b/src/mc_view/PDBfile.java
@@ -20,6 +20,13 @@
  */
 package mc_view;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
@@ -28,12 +35,6 @@ import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.util.MessageManager;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
 public class PDBfile extends StructureFile
 {
   private static String CALC_ID_PREFIX = "JalviewPDB";
@@ -51,7 +52,9 @@ public class PDBfile extends StructureFile
           DataSourceType sourceType) throws IOException
   {
     super(false, dataObject, sourceType);
+    Console.debug("***** PDBfile constructor");
     addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    Console.debug("***** About to doParse() 1");
     doParse();
   }
 
@@ -60,6 +63,7 @@ public class PDBfile extends StructureFile
   {
     super(false, source);
     addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    Console.debug("***** About to doParse() 2");
     doParse();
   }
 
@@ -152,10 +156,11 @@ public class PDBfile extends StructureFile
           if (tmpchain != null)
           {
             tmpchain.atoms.addElement(tmpatom);
-          } else
+          }
+          else
           {
-            // PDBfile never handles alphafold models, so false
-            tmpchain = new PDBChain(getId(), tmpatom.chain, false);
+            // PDBfile never handles alphafold models
+            tmpchain = new PDBChain(getId(), tmpatom.chain);
             getChains().add(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }