From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 9 Sep 2016 10:49:35 +0000 (+0100)
Subject: merge
X-Git-Tag: Release_2_10_0~47
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4687a9d3adb02abca831fbb119a54153bc2a19ca;p=jalview.git

merge
---

4687a9d3adb02abca831fbb119a54153bc2a19ca
diff --cc help/html/features/viewingpdbs.html
index 61c13c4,e62b2a7..edb3762
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@@ -46,12 -45,13 +45,13 @@@
          </li>
        </ul>
      </li>
-     <li><strong>Selecting Structures</strong><br /> If structures
-       have been discovered, then some will already be selected according
-       to predefined selection criteria, such as structures with the
-       highest resolution. Use the drop down menu to select structures
-       according to different criteria, or, alternatively, choose
-       structures manually by selecting with the keyboard and mouse.
+     <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
+       'highest resolution', simply choose another to pick structures in
+       a different way.<br />
        <ul>
          <li><strong>Viewing Cached Structures</strong><br />If you
            have previously downloaded structures for your sequences, they
@@@ -107,17 -106,19 +106,18 @@@
  
  
    <p>
-     <strong>Importing PDB Entries or files in PDB format</strong><br>
-     You can retrieve sequences from the PDB using the <a
-       href="pdbsequencefetcher.html"
-     >Sequence Fetcher</a>. Any sequences retrieved with this service are
-     automatically associated with their source database entry. For PDB
-     sequences, simply select PDB as the database and enter your known
-     PDB id (appended with ':' and a chain code, if desired).<br>
-     Jalview will also read PDB files directly. Simply load in the file
-     as you would an alignment file. The sequences of any protein or
-     nucleotide chains will be extracted from the file and viewed in the
-     alignment window.
+     <strong>Retrieving sequences from the PDB</strong><br>You can
+     retrieve sequences from the PDB using the <a
+       href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
+     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
+     will be extracted from the file and viewed in the alignment window.
    </p>
  
    <p>
@@@ -163,6 -151,21 +150,21 @@@
        Features"</strong> menu item and the <a href="featuresettings.html">Feature
        Settings dialog box</a>.
    </p>
+   <br/>
+   <hr>
+   <p>
+     <strong>Switching between mmCIF and PDB format for
+       downloading files from the PDB</strong><br /> Jalview now employs the <a
+       href="mmcif.html">mmCIF format</a> for importing 3D structure data
+     from flat file and EMBL-PDBe web-service, as recommended by the
+     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>
+   </p>
  
    <p>
      <em><strong>Outstanding problem with cut'n'pasted