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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
The Jalview internal PDB Viewer
+Since Jalview 2.3, the Jmol PDB Viewer is
+the main method for viewing PDB
+structures. The documentation below concerns the original Jalview
+PDB viewer, which is only used in situations where Jmol is unavailable
+or cannot operate.
The PDB Viewer Window +
This interactive structure viewing window is opened by selecting +entries from the "Structure→" submenu + of the sequence + id pop-up menu. The internal PDB viewer is not able to show + superpositions, so no other options are provided. Structures can only + be viewed for sequences which have an associated +PDB structure, and the PDB Viewer will only be associated with the +particular alignment view from which it was opened.
+Controls
+The structure is rendered as an alpha-carbon trace. Moving the +mouse over the structure brings up tooltips with a residue name and PDB +sequence position. If a mapping exists to a residue in the associated +sequence, then this will be highlighted in the associated view in its +alignment window, and vice versa for viewing the coordinates associated +with a particular residue in the sequence in a particular view on the +alignment.
+Selecting a residue highlights its associated sequence residue +and alpha carbon location.
++
Action | +Windows | +Unix | +Mac/OSX | +
Select/ + Deselect + Residue |
+ Left Click | +Left Click | +Click | +
Rotate View | +Left Click and Drag | +Left Click and Drag | +Click and Drag | +
Roll View | +Right Click and drag | +Right Click and Drag | +TODO | +
Move Origin | +Middle-Button and Drag | +Middle-Button and Drag | +TODO | +
Zoom In | +Up Arrow | +Up Arrow | +Up Arrow | +
Zoom Out | +Down Arrow | +Down Arrow | +Down Arrow | +
There are three menus: +
Notes for PDB Viewing in the Jalview Applet +
The applet can only load PDB files by copying and pasting the +text into the popup window which appears when "Show PDB +Structure" is selected after right clicking on a sequence name.
+ +