X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbsequencefetcher.html;h=bb63bed722df52b12e23e44b06ce3404c4f270f9;hb=refs%2Fheads%2Fbug%2FJAL-3202zerosInProfile;hp=0412a5fb4d70a9a0f27c1d119c4c53793e1cd53c;hpb=d709b26b0decca4a43788c225fef897818826ef9;p=jalview.git diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html index 0412a5f..bb63bed 100644 --- a/help/html/features/pdbsequencefetcher.html +++ b/help/html/features/pdbsequencefetcher.html @@ -20,64 +20,87 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. -->
-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 ++ 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"). +
+ -- 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. -
++ 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 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. -
++ 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 +