X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=1737abe987312b21e48c46d92ffcd68c8b7acab9;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=c1c6ae79fe3c4f98b1d361570dbcc8269c4fd3c9;hpb=8d0464e6227795ef73b337205ce7f586976bb70c;p=jalview.git
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PDB Viewer
-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:
-
- - 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.
+
+
+
+
+ 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.