X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=9e1e6e5275cfc34edf693f73e51de7d0f33c0a5c;hb=bb5c8d98be1c4965b1a43b97f05b07e9ceb10343;hp=bd240ea4bd2b9d4ea492dfdfd309c40296771af2;hpb=f850089f8bc67403194f4a1a3b793a46dbb4224a;p=jalview.git
diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html
index bd240ea..9e1e6e5 100755
--- a/help/html/features/pdbviewer.html
+++ b/help/html/features/pdbviewer.html
@@ -1,93 +1,137 @@
-
-
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 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.
+
+