X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=bb5c1659441b805e9db85eef87060b1b80091083;hb=1f9ca4896d57bfb16a25c87cfc0b8cd19fcdf148;hp=e4326d1ee4047c706a407a901369fbadb0d61773;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index e4326d1..bb5c165 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -165,8 +165,8 @@ public class Pdb extends EbiFileRetrievedProxy
       // todo get rid of Type and use FileFormatI instead?
       FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
               : FileFormat.MMCif;
-      pdbAlignment = new FormatAdapter().readFile(file, DataSourceType.FILE,
-              fileFormat);
+      pdbAlignment = new FormatAdapter().readFile(tmpFile,
+              DataSourceType.FILE, fileFormat);
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();