From: tcofoegbu Date: Wed, 15 Jul 2015 13:25:15 +0000 (+0100) Subject: JAL-1667 JAL-1668 updated reviewed and updated docs X-Git-Tag: Release_2_10_0~573 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c248aad32a357e7440b2e5ab3ea8c5fddbb26b84;p=jalview.git JAL-1667 JAL-1668 updated reviewed and updated docs --- diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html index 15dc2c6..990a1c9 100644 --- a/help/html/features/pdbsequencefetcher.html +++ b/help/html/features/pdbsequencefetcher.html @@ -25,12 +25,12 @@ PDB Sequence Fetcher -

From Jalview 2.x.x a speciliased interface was introduced for +

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 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 @@ -40,17 +40,18 @@

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

- 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: +

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 retrieve a specific chain for a PDB entry, append the PDB ID with a @@ -81,12 +82,12 @@
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 + 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. + 2.9
\ No newline at end of file diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index 7dd69c1..039fdb0 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -102,7 +102,7 @@

- The Structure Chooser interface was introduced in Jalview 2.x.x. + The Structure Chooser interface was introduced in Jalview 2.9.