PDB Sequence Fetcher

From: tcofoegbu Date: Wed, 22 Apr 2015 15:46:46 +0000 (+0100) Subject: JAL-1667_1668 added help documentation for PDB Sequence fetcher X-Git-Tag: Jalview_2_9~56^2~1^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d709b26b0decca4a43788c225fef897818826ef9;p=jalview.git JAL-1667_1668 added help documentation for PDB Sequence fetcher --- diff --git a/help/html/features/pdbseqfetcher.png b/help/html/features/pdbseqfetcher.png new file mode 100644 index 0000000..b243168 Binary files /dev/null and b/help/html/features/pdbseqfetcher.png differ diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html new file mode 100644 index 0000000..0412a5f --- /dev/null +++ b/help/html/features/pdbsequencefetcher.html @@ -0,0 +1,83 @@ + + + +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. +

+ +

PDB sequence fetcher (introduced in Jalview 2.x.x)

+ + +

+ 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'. +
+ +
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. +

+ + \ No newline at end of file diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index fa61e1a..68c5520 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -49,6 +49,7 @@ WSDBFetch service provided by the European Bioinformatics Institute, or, since J one or more accession ids (as a semi-colon separated list), or press the "Example" button to paste the example accession for the currently selected database into the retrieval box. Finally, press "OK" to initiate the retrieval.

Since Jalview 2.x.x if PDB is selected as the sequence database, a specialised interface - PDB Sequence Fetcher is used for discovering and retrieving the sequenec data.

Specifying chains for PDB IDs If you are retrieving sequences from the PDB, you can retrieve specific chains by appending a colon and the chain id to the PDB diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index 830c801..7dd69c1 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -102,7 +102,7 @@

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