X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbsequencefetcher.html;h=925127728d8d5aeaea1ae142cdd812e798672193;hb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;hp=0a7802ec207a28493604ca7024f5ed90b04fc5d0;hpb=d26d84a079b512973f50703ff2367a62da9efc2e;p=jalview.git diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html index 0a7802e..9251277 100644 --- a/help/html/features/pdbsequencefetcher.html +++ b/help/html/features/pdbsequencefetcher.html @@ -20,75 +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'.
- Furthermore, the PDB search interface also provides the following
- functionalities:
-
- 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 +