X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=834cac56abeff0858b572a9e8c254c8a12fe8874;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=bd240ea4bd2b9d4ea492dfdfd309c40296771af2;hpb=f850089f8bc67403194f4a1a3b793a46dbb4224a;p=jalview.git
diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html
index bd240ea..834cac5 100755
--- a/help/html/features/pdbviewer.html
+++ b/help/html/features/pdbviewer.html
@@ -1,93 +1,176 @@
-
-PDB Viewer
-
-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.
-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 alignment window, and vice versa for viewing the coordinates
-associated with a particular residue in the sequence.
-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
-alignment window, 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.
-
-
+
+
+
+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.
+
+