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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
Viewing PDB Structures
++ Viewing PDB Structures +
+ Jalview can be used to view protein structures by following the steps below: +Jalview can view protein structures associated with a sequence -via the "Structure→View PDB entry:" entries from a -sequence's pop-up menu. Once a pdb + The + Jmol viewer has been included since Jalview + 2.3. Jalview 2.8.2 included support for Chimera, provided it is + installed and can be launched by Jalview. The default viewer can be + configured in the + Structure tab in the + Tools→Preferences dialog box. +
+ Structure data imported into Jalview can also be processed to display + secondary structure and temperature factor annotation. See the Annotation from Structure page for + more information. +
+ + +If a single pdb structure is selected, one of the following will happen:
- Additionally, if several of the sequences in the currently selected - region of the alignment have associated structures, then Jalview will - provide a 'View X structures' entry in the submenu. This - option will open a new Jmol view containing all the structures - available for all selected sequences, superimposed using the currently - selected region of the alignment. (This capability was added - in Jalview 2.7) -
- -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 Note: This feature was added in Jalview 2.7
Note for jalview applet users: 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.