JAL-1711 and JAL-1714 documentation updated

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

diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html
index 0412a5f..0a7802e 100644 (file)
--- a/help/html/features/pdbsequencefetcher.html
+++ b/help/html/features/pdbsequencefetcher.html
@@ -39,42 +39,53 @@
                        Retrieval Source'</strong> interface of <a href="seqfetch.html">Sequence
                        Fetcher</a>.
        </p>
+       <br>
 
        <img src="pdbseqfetcher.png" align="left"
                alt="PDB sequence fetcher (introduced in Jalview 2.x.x)">
 
-
+       <br>
        <p>
                <strong>Searching the PDB Database</strong><br> Once the
                interface is opened, typing in the search text box will execute a live
                query to the PDB database and display the results on-the-fly as seen
                in the screen-shot above. Use the drop-down menu to select a specific
                field to search by in the PDB database, the default option is <strong>'ALL'</strong>.
-       <br>
-       
-       <br>Wild card searching: The PDB sequence fetcher also provides support for wild card querying of the PDB database.
-       <br>Single character (matches a single character) - ?
- The search string te?t would match both test and text.
+               Furthermore, the PDB search interface also provides the following
+               functionalities:
+       <ul>
+               <li>Retrieving a unique chain for a PDB entry: <br>To
+                       retrieve a specific chain for a PDB entry, append the PDB ID with a
+                       colon followed by the chain code in the search box. eg: 1xyz:A
+               </li>
 
-<br>Multiple characters (matches zero or more sequential characters) - *
+               <li>Querying multiple PDB Id's in one operation:<br>The PDB
+                       search interface supports querying of multiple PDB Ids in one
+                       operation by separating the list of PDB Ids with a semi-colon i.e:
+                       1xyz;2xyz;3xyz
+               </li>
 
-The wildcard search:
-tes*  - would match test, testing, and tester.
-
-
-You can also use wildcard characters in the middle of a term. For
-example:
-te*t - would match test and text.
-*est  - would match pest and test.
- </p>
- 
+               <li>Wild card searching: <br>The PDB sequence fetcher also
+                       provides support for wild card querying of the PDB database. <br>Single
+                       character (matches a single character) - ? The search string te?t
+                       would match both test and text. <br>Multiple characters (matches
+                       zero or more sequential characters) - * The wildcard search: tes* -
+                       would match test, testing, and tester. You can also use wildcard
+                       characters in the middle of a term. For example: te*t - would match
+                       test and text. *est - would match pest and test.
+               </li>
+       </ul>
+       <p>
+               <strong>Customising displayed meta-data</strong> <br>To change
+               the displayed meta-data in the search result, click the <strong>'Configure
+                       Displayed Columns'</strong> tab, then tick off the options wanted.
+       </p>
        <p>
-               <strong>Customising displayed meta-data</strong> <br>To change the
-               displayed meta-data in the search result, click the <strong>'Configure
-                       Displayed Columns'</strong> tab, then tick off the options wanted. 
+               <strong>Importing Sequence</strong><br> After querying the PDB
+               database, to import the found data into Jalview, select the entries
+               you wish to import then click the ok button at the bottom of the
+               interface.
        </p>
-       <p><strong>Importing Sequence</strong><br>
-       After querying the PDB database, to import the found data into Jalview, select the entries you wish to import then click the ok button at the bottom of the interface.</p>
        <p>
                <em>The PDB Sequence Fetcher interface was introduced in Jalview
                        2.x.x.</em>