Viewing PDB Structures
-Jalview has a simple 3D structure viewer which - can visualize polypeptide backbone structures associated with a sequence in - a particular alignment view. It is accessed via the "Strucutre→View - PDB entry:" entry from the sequence's pop-up menu.
-Since Jalview 2.3, Jmol has been integrated into the application and will also - run in the applet in all latest web browsers. For more help using Jmol, see - http://jmol.sourceforge.net/docs/JmolUserGuide/ -
-To associate PDB files with a sequence, right click on a sequence ID and select - "Structure→ Associate Structure with Sequence", - and one of the submenus:
-Note: You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with this - service are automatically associated with their source database entry. For PDB - sequences, simply select PDB as the database and enter your known PDB id (appended - with ':' and a chain code, if desired).
-Sequences which have PDB File associations are annotated with sequence features - from the group 'PDBFile' giving the corresponding PDB Residue Number for each - mapped residue in the seuqence. The display of these features is controlled through - the "View→Sequence Features" menu item and the - Feature Settings dialog box.
-See the PDB Viewer help page for more information.
- - + + +Viewing PDB Structures
+Jalview can view protein structures associated with a sequence via the "Structure→View + PDB entry:" entries from a sequence's pop-up menu. This will open an + interactive display of the structure in a new window, or prompt you + to associate the sequence with an existing view of the selected + structure. See the Jmol PDB viewer help page + for more information about the display. +
+To associate PDB files with a sequence, right click on a sequence ID and select + "Structure→ Associate Structure with Sequence", + and one of the submenus:
+Importing PDB Entries or files in PDB format
+You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with this
+ service are automatically associated with their source database entry. For PDB
+ sequences, simply select PDB as the database and enter your known PDB id (appended
+ with ':' and a chain code, if desired).
+
Jalview will also read PDB files directly. Simply load in the file
+as you would an alignment file. The sequences of any peptide chains
+will be extracted from the file and viewed in the alignment window.
+
Note for jalview applet users: due to the applet security
+constraints, PDB Files can currently only be imported by cut and paste
+of the PDB file text into the text box opened by the 'From File' entry
+of the structure menu.
Viewing the PDB Residue Numbering
+Sequences which have PDB entry or PDB file associations are annotated
+with sequence features from a group named with the associated PDB
+accession number or file name. Each feature gives the corresponding
+PDB Residue Number for each mapped residue in the seuqence. The
+display of these features is controlled through the
+"View→Sequence Features" menu item
+and the Feature Settings dialog
+box.