X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbsequencefetcher.html;h=1db7176966f3dc892636681e267b1868a2facbaa;hb=e50faa2d7e8c3d056955be397920c17bcf99bcf7;hp=ce7d96e147df67255f7fc90dc2a9be8e357a12d8;hpb=0c6d48fc655b08e80941576156004926dd253c23;p=jalview.git 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. -->
-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:
-+ 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. +
++
- 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 - 2.9 -
+ Customising The PDB Sequence FetcherTo 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 +