If you + want to find structures based on a specific PDB metadata field, + you can select it from the drop-down menu.
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
-
- -
- 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:
-
-
-
-
- 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 -
+ - 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.
- - 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
-
- - 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. -
+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.
+
For example: te*t - would match test and text. + *est - would match pest and test.
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.