The PDB Viewer Window
This interactive structure viewing window is opened by selecting
the "Sequence→View PDB entry:" entry in
the sequence id pop-up menu. This
can only be done 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:
- File
- Save As
Saves the current view as an EPS or PNG file.
- View Mapping
Opens a text window showing the alignment between the
residues corresponding to alpha-carbon atoms in the PDB structure and
the residues in the associated sequence.
- Colours
- By Sequence
Colours each residue in the structure with the colour of its
corresponding residue in the associated sequence as rendered in the
associated alignment view, including any Uniprot sequence features or
region colourings.
Residues which only exist in the PDB structure are coloured white if
they are insertions (relative to the associated sequence in the
alignment) and grey if they are N or C terminal flanks outside the
region mapped to the alignment window's sequence.
- By Chain
Assigns a random colour to each PDB chain.
- Charge & Cysteine
Highlights cysteines in yellow, anionic (Aspartic Acid or
Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
residues in blue.
- Standard and User Defined Jalview
colourschemes.
The remaining entries apply the colourschemes available from the
standard and user defined amino
acid colours.
- View
These options can be turned off to improve performance when
viewing large structures, some at the expense of visual clarity.
- Wireframe
Draws thin lines rather than thick lines for the
alpha-carbon trace.
- Depthcue
Shades the structure so parts of the structure near the front
of the view are brighter than those further away.
- Z Buffering
Applies depth sorting to correctly render occluded regions
of the backbone trace.
- Show All Chains
When turned on, shows all chains in the PDB file, not just
the one associated with a sequence in the alignment window.
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.