JAL-1544 'Jalview' consistently capitalised

[jalview.git] / help / html / features / viewingpdbs.html

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index bece211..44a07cc 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -29,18 +29,17 @@
        Jalview can be used to view protein structures by following the steps below:
        <ol>
                <li>Select the <strong>"View Structure"</strong> option from a
-                       sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.
+                       sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
                        <ul>
-                               <li>If one or more structures exists for the given sequence, the <strong>'Structure Chooser'</strong>
+                               <li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
                                        dialogue is opened with a list of the found structures meta-data.</li>
-                               <li>However, if no structure was found, the <strong>'Structure Chooser'</strong> dialogue is opened with options for manual association of PDB structures.</li>
+                               <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface is opened with options for manual association of PDB structures.</li>
                        </ul> 
                        </li>
-               <li>Choose the structure to view from the presented structures
-                       summary list. This can be done either manually by clicking directly
-                       on the desired structure from the list, or automatically by
-                       using the filter combo-box which enables filtering on certain
-                       criteria like quality, resolution, etc. The best structure for the chosen criteria is automatically selected by the filtration process. </li>
+               <li>Choose the structure to view from the discovered list. This can be done either manually by clicking directly
+                       on the desired structure(s) in the list, or automatically by
+                       using the drop-down menu on the interface to filter and auto-select the best structure based on certain
+                       criteria like quality, resolution, etc.</li>
                <li>When the desired structure(s) have been selected, they can be
                        viewed by clicking the <strong>"View"</strong> button below the summary list.
                </li> 
@@ -101,27 +100,7 @@ structure is selected, one of the following will happen:</p>
        <li style="list-style: none">See the <a href="jmol.html">Jmol
        </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
 </ul>
-       <p><strong>Associating PDB files with Sequences</strong></p>
-       <p>Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the <strong>"View Structure"</strong> option is selected
-       from a sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Jalview uses the sequence's ID to query the PDB Rest API, provided by the
-       EBI to discover PDB ids associated with the sequence. </p>
-       
-       <p><strong>Manual association of PDB files with Sequences</strong> </p>
-       <p>To manually associate PDB files with a sequence, right click on a sequence
-ID and select  the <strong>"View Structure"</strong> option, this opens the <strong>'Structure Chooser'</strong> dialogue. Then pick any of the follwing options listed below from the drop-down menu in the <strong>'Structure Chooser'</strong> panel to proceed with manual association:
 
-<ul>
-       <li><strong>From File</strong> - You can load a PDB file from the local machine or
-       network and associate it with the selected sequence. PDB files
-       associated in this way will also be saved in the <a
-               href="jalarchive.html">Jalview Archive file</a>.<br>
-       </li>
-       <li><strong>Enter PDB Id</strong> - Jalview will use the PDB Rest API, provided by the
-       EBI, to fetch the PDB file with the entered Id.<br>
-       </li>
-</ul>
-
-<strong>Note:</strong> The drop-down menu in the 'Structure Chooser' panel may contain other options employed for filtering structures when one or more structures are auto-discovered.
 
 <p><strong>Importing PDB Entries or files in PDB format</strong><br>
 You can retrieve sequences from the PDB using the <a
@@ -145,7 +124,7 @@ associate PDB files with names like '1gaq.pdb' with sequences that
 have an ID like '1gaq'.
 <br/><em>Note: This feature was added in Jalview 2.7</em>
 </p>
-<p><em>Note for jalview applet users:<br>
+<p><em>Note for Jalview applet users:<br>
 Due to the applet security constraints, PDB Files can currently only be
 imported by cut and paste of the PDB file text into the text box opened
 by the 'From File' entry of the structure menu.</em></p>