merge

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index e62b2a7..edb3762 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -46,7 +46,7 @@
       </ul>
     </li>
     <li><strong>Selecting Structures</strong><br />You can select
-      the structures to you want to open and view by selecting them with
+      the structures that you want to open and view by selecting them with
       the mouse and keyboard.<br />By default, if structures were
       discovered, then some will already be selected according to the
       criteria shown in the drop-down menu. The default criteria is
@@ -112,9 +112,8 @@
     retrieved with this service are derived directly from the PDB 3D
     structure data, which can be viewed in the same way above. Secondary
     structure and temperature factor annotation can also be added. <br />
-  </p>
-  <p>
-    <strong>Retrieving sequences from the PDB</strong><br>Jalview
+ 
+ <br>Jalview
     will also read PDB files directly - either in PDB format, or <a
       href="mmcif.html">mmCIF</a>. Simply load in the file as you would
     an alignment file. The sequences of any protein or nucleotide chains
@@ -161,7 +160,7 @@
     wwwPDB. If you prefer (for any reason) to download data as PDB files
     instead, then first close Jalview, and add the following line to
     your .jalview_properties file:<br />
-    <code> DEFAULT_STRUCTURE_FORMAT=PDB </code>
+    <code> PDB_DOWNLOAD_FORMAT=PDB </code>
     <br /> When this setting is configured, Jalview will only request
     PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
       file support was added in Jalview 2.10.</em>

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index df71ccc..508e8a7 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -232,7 +232,7 @@ public class Cache
   /**
    * Allowed values are PDB or mmCIF
    */
-  private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+  private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
           .toString();
 
   private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
@@ -445,7 +445,7 @@ public class Cache
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
             .getDefault(
-            "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
+"PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
     StructureImportSettings
             .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
                     "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index fda0198..c1d1144 100644 (file)
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -64,7 +64,7 @@ public class PDBSequenceFetcherTest
   {
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_FORMAT",
+    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT",
             "PDB");
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");