PDB Sequence Fetcher

From e50faa2d7e8c3d056955be397920c17bcf99bcf7 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 9 Sep 2015 16:56:04 +0100 Subject: [PATCH] JAL-1645 JAL-1667 revised PDB sequence fetcher docs --- help/html/features/pdbsequencefetcher.html | 111 ++++++++++++++-------------- 1 file changed, 55 insertions(+), 56 deletions(-) diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html index ce7d96e..1db7176 100644 --- a/help/html/features/pdbsequencefetcher.html +++ b/help/html/features/pdbsequencefetcher.html @@ -20,72 +20,71 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -PDB Sequence Fetcher +The PDB Sequence Fetcher - PDB Sequence Fetcher -

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 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.

- The PDB Sequence Fetcher interface can be accessed from "File →Fetch Sequence(s) →Select Database →PDB" click the ok button after selecting PDB from the 'Select Database - Retrieval Source' interface. -

+ 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"). +

+ alt="PDB sequence fetcher (introduced in Jalview 2.9)"/>

Searching the PDB Database

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.

- -

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 +
+ To search the PDB, begin typing in the text box. The results of your + query are shown in the search results tab, which updates every time + you type in the search text box. 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. eg: 1xyz: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 by separating them with a semi-colon.
  e.g. + 1xyz;2xyz;3xyz
  Hitting Return or OK will automatically fetch + those IDs, like the default Sequence Fetcher interface.
- 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. -
+
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.

- The PDB Sequence Fetcher interface was introduced in Jalview - 2.9 -

+ 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 +

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