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"). +

PDB sequence fetcher (introduced in Jalview 2.9) -

+ 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:

-

- 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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