<body>
<strong>PDB Sequence Fetcher</strong>
- <p>From Jalview 2.x.x a speciliased interface was introduced for
+ <p>From Jalview 2.9, a specialised interface was introduced for
fast and efficient discovery/retrieval of sequence data from the PDB
database. The introduced interface enables live querying of PDB data
on-the-fly thereby eliminating the need to memorise database accession
- or to cross-reference other bioinformatics websites before retrieving
- a sequence data in jalview. The underlying technology is provided by
+ or to manually cross-reference other bioinformatics websites before retrieving
+ sequence data in Jalview. The underlying infrastructure is provided by
EBI and is based on Apache Solr which is a text based search engine.</p>
-
<p>
- The PDB Sequence Fetcher interface can be opened by selecting <strong>PDB</strong>
- as the choice database from the <strong>'Select Database
- 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>
+ The PDB Sequence Fetcher interface can be accessed from <b>"File →Fetch Sequence(s) →Select Database →PDB"</b> click the ok button after selecting PDB from the 'Select Database
+ Retrieval Source' interface.
+ </p>
<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.
-
-<br>Multiple characters (matches zero or more sequential characters) - *
+ <img src="pdbseqfetcher.png" align="left"
+ alt="PDB sequence fetcher (introduced in Jalview 2.9)">
+ </p>
-The wildcard search:
-tes* - would match test, testing, and tester.
+ <p><strong>Searching the PDB Database</strong></p>
+ <p>When the interface is opened, a live query to the PDB database is
+ executed every time a character is typed into the search text box, and
+ a result is displayed on-the-fly as seen in the screenshot above.</p>
+
+ <p>Use the drop-down menu to select a specific field to search by in the PDB database, the default
+ option is 'ALL'.</p>
+
+ <p> Furthermore, the PDB search interface also provides the following functionalities:</p>
+ <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>
+ <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>
-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 'Configure
+ Displayed Columns' 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>
+ 2.9</em>
</p>
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