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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.
+ +