biojava
diff --git a/‎biojava-structure/src/main/java/org/biojava/nbio/structure/Compound.java‎
Lines changed: 16 additions & 7 deletions b/‎biojava-structure/src/main/java/org/biojava/nbio/structure/Compound.java‎
Lines changed: 16 additions & 7 deletions
diff --git a/‎biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java‎
Lines changed: 9 additions & 7 deletions b/‎biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java‎
Lines changed: 9 additions & 7 deletions
@@ -32,6 +32,8 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
 
 /**
  * An object to contain the info from the PDB header for a Molecule.
@@ -418,17 +420,23 @@ public void showSource() {
 	}
 
 	/**
-	 * Return the list of member chain IDs that are described by this Compound 
-	 * @return the list of ChainIDs that are described by this Compound
+	 * Return the list of member chain IDs that are described by this Compound, 
+	 * only unique chain IDs are contained in the list. 
+	 * Note that in the case of multimodel structures this will return just the unique
+	 * chain identifiers whilst {@link #getChains()} will return a corresponding chain 
+	 * per model. 
+	 * @return the list of unique ChainIDs that are described by this Compound
 	 * @see #setChains(List)
 	 * @see #getChains()
 	 */
 	public List<String> getChainIds() {
-		List<String> chainIds = new ArrayList<String>();
-		for (Chain chain : chains) {
-			chainIds.add(chain.getChainID());
+		
+		Set<String> uniqChainIds = new TreeSet<String>();
+		for (int i=0;i<getChains().size();i++) {
+			uniqChainIds.add(getChains().get(i).getChainID());
 		}
-		return chainIds;
+
+		return new ArrayList<String>(uniqChainIds);
 	}
 
 	/**
@@ -812,7 +820,8 @@ public void setExpressionSystemOtherDetails(String expressionSystemOtherDetails)
 	}
 
 	/** 
-	 * Get the list of chains that are part of this Compound
+	 * Get the list of chains that are part of this Compound. Note that for multi-model 
+	 * structures chains from all models are returned.
 	 *
 	 * @return a List of Chain objects
 	 */
 
@@ -170,15 +170,17 @@ public Structure clone() {
 		for (Compound compound:this.compounds) {
 			Compound newCompound = new Compound(compound); // this sets everything but the chains
 			for (String chainId:compound.getChainIds()) {
-				try {
+				
 					for (int modelNr=0;modelNr<n.nrModels();modelNr++) {
-						Chain newChain = n.getChainByPDB(chainId,modelNr);
-						newChain.setCompound(newCompound);
-						newCompound.addChain(newChain);
+						try {
+							Chain newChain = n.getChainByPDB(chainId,modelNr);
+							newChain.setCompound(newCompound);
+							newCompound.addChain(newChain);
+						} catch (StructureException e) {
+							// this actually happens for structure 1msh, which has no chain B for model 29 (clearly a deposition error)
+							logger.warn("Could not find chain id "+chainId+" of model "+modelNr+" while cloning compound "+compound.getMolId()+". Something is wrong!");
+						}
 					}
-				} catch (StructureException e) {
-					logger.error("Could not find chain id {} while cloning Structure's compounds. Something is wrong!", e);
-				}
 			}
 			newCompoundList.add(newCompound);
 		}