X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbsequencefetcher.html;h=925127728d8d5aeaea1ae142cdd812e798672193;hb=e1cb1f4ff4ae05504c806d99395358629c807956;hp=15dc2c60d668ca7c4d2cdcbb48bcecc5285c338c;hpb=bc27e1b604af729b363da1f29bdd5774ca79f4e4;p=jalview.git
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@@ -20,73 +20,87 @@
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-PDB Sequence Fetcher
+The PDB Sequence Fetcher
- PDB Sequence Fetcher
- From Jalview 2.x.x a speciliased 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
- EBI and is based on Apache Solr which is a text based search engine.
-
- The PDB Sequence Fetcher interface can be opened by selecting PDB
- as the choice database from the 'Select Database
- Retrieval Source' interface of Sequence
- Fetcher.
-
-
- 
-
+ The PDB Sequence Fetcher
+
+ Jalview provides a specialised interface that allows fast and
+ efficient discovery and retrieval of data from the PDB database,
+ based on the EMBL-EBI's PDBe BioSOLR query interface. It allows
+ interactive querying of PDB metadata with free text and structured
+ queries, so structures can be located without prior knowledge of
+ their database accessions, or via manual cross-referencing
+ with other bioinformatics websites.
+
+
+ To open the PDB Sequence Fetcher, select PDB as the database from
+ any Sequence Fetcher dialog (opened via
+ "File →Fetch Sequences").
+
+
- Searching the PDB Database
-
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
- 'ALL'. Furthermore, the PDB search interface also
- provides the following functionalities:
-
- - Retrieving a unique chain for a PDB entry:
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
-
+
+ Searching the PDB Database
+
+ To search the PDB, begin typing in the text box. If the
+ 'autosearch' checkbox is enabled, then the results of your query
+ will be automatically updated and shown in the search results tab;
+ otherwise, press return to update the results. To access previous
+ searches, press the down-arrow or click the drop down menu icon at
+ the side of the search box. If you just want to paste in a list of
+ IDs, the 'Retrieve IDs' tab provides a batch-retrieval interface.
+
+ You can sort results according to the displayed columns, and select
+ entries with the mouse and keyboard. Once you have selected one or
+ more entries, hit the OK button to retrieve and
+ view them in Jalview.
+
+
+
+ - Searching a specific PDB field
If
+ you want to find structures based on a specific PDB metadata
+ field, you can select it from the drop-down menu.
+ - Retrieving a unique chain for a PDB entry
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.
e.g
+ 1xyz:A
- - Querying multiple PDB Id's in one operation:
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
-
+ - Bulk PDB retrieval
Multiple PDB
+ IDs can be specified for retrieval via the
+ Retrieve IDs tab.
- - Wild card searching:
The PDB sequence fetcher also
- provides support for wild card querying of the PDB database.
Single
- character (matches a single character) - ? The search string te?t
- would match both test and text.
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.
-
-
-
- Customising displayed meta-data
To change
- the displayed meta-data in the search result, click the 'Configure
- Displayed Columns' tab, then tick off the options wanted.
-
-
- Importing Sequence
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.
-
-
- The PDB Sequence Fetcher interface was introduced in Jalview
- 2.x.x.
-
+ - Wild card searching
The following
+ wild cards are supported by the EMBL-EBI PDBe query service:
+
+ - ? matches a single character
The
+ search string te?t would match both test and text.
+ - * matches multiple characters
The
+ search string: tes* - would match test, testing, and tester.
+
Note: you can use wildcard characters anywhere in a
+ query string.
For example: te*t - would match test and text.
+ *est - would match pest and test.
+ - Structured queries
The PDBe SOLR
+ interface supports boolean query syntax, allowing quoted search
+ strings to be combined with AND, OR, and NOT. Currently, no
+ special support for constructing these queries is provided in the
+ query dialog box.
+
+
+ Customising The PDB Sequence Fetcher
+
+
+ To change the displayed meta-data in the search result, click the
+ 'Configure Displayed Columns' tab, and select the fields you'd like
+ displayed. These fields can also be configured via the
+ Structure tab of the Jalview
+ Desktop Preferences.
+
+
+ The PDB Sequence Fetcher interface was introduced in
+ Jalview 2.9
+