PDB Sequence Fetcher

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbsequencefetcher.html;h=c26575e62fa1f8061929e9345db8726f3e02b085;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=ce7d96e147df67255f7fc90dc2a9be8e357a12d8;hpb=d829cd0ed80c9888a868a847d1e086671f6c6cc3;p=jalview.git diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html index ce7d96e..c26575e 100644 --- a/help/html/features/pdbsequencefetcher.html +++ b/help/html/features/pdbsequencefetcher.html @@ -1,7 +1,7 @@ -PDB Sequence Fetcher +The PDB Sequence Fetcher - PDB Sequence Fetcher -

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. -

- PDB sequence fetcher (introduced in Jalview 2.9) -

+ 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"). +

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:

Retrieving a unique chain for a PDB entry:
To - retrieve a specific chain for a PDB entry, append the PDB ID with a - colon followed by the chain code in the search box. eg: 1xyz:A -

+ Searching the PDB Database +

+ 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. +

Searching a specific PDB field
If you + want to find structures based on a specific PDB metadata field, + you can select it from the drop-down menu.
Retrieving a unique chain for a PDB entry
To + retrieve a specific chain for a PDB entry, append the PDB ID with + a colon followed by the chain code in the search box.
e.g + 1xyz:A
Querying multiple PDB Id's in one operation:
The PDB - search interface supports querying of multiple PDB Ids in one - operation by separating the list of PDB Ids with a semi-colon i.e: - 1xyz;2xyz;3xyz -
Bulk PDB retrieval
Multiple PDB + IDs can be specified by separating them with a semi-colon.
+ e.g. 1xyz;2xyz;3xyz
Hitting Return or OK will automatically + fetch those IDs, like the default Sequence Fetcher interface.
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 - 2.9 -

Wild card searching
The following + wild cards are supported by the EMBL-EBI PDBe query service: +
- ? matches a single character
  The + search string te?t would match both test and text.
- * matches multiple characters
  The + search string: tes* - would match test, testing, and tester.
Note: you can use wildcard characters anywhere in a + query string.
For example: te*t - would match test and text. + *est - would match pest and test.
Structured queries
The PDBe SOLR + interface supports boolean query syntax, allowing quoted search + strings to be combined with AND, OR, and NOT. Currently, no + special support for constructing these queries is provided in the + query dialog box.

+ 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 +

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