X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=fc69f9ba2ce3d82f4e82d8806056021b3abfb457;hb=3b25289f07fabf37d51cfde2687df93fe8e8c129;hp=a7e2c108442a85413d4919c35eaf33ed754f1d0d;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git
diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html
index a7e2c10..fc69f9b 100755
--- a/help/html/features/pdbviewer.html
+++ b/help/html/features/pdbviewer.html
@@ -1,45 +1,143 @@
-
-PDB Viewer
-
-Viewing PDB Structures
-Jalview has a simple 3D structure viewer which can load PDB files and associate
- the structure with a sequence in an alignment.
-There are 2 ways to load and associate a PDB file into Jalview application.
-
- - Select "Sequence Features" from
- the "View" menu. This will attempt to match your sequences with
- the Uniprot database first by name, then by sequence. The same process will
- make note of any PDB files associated with each sequence.
- - Select "Fetch Sequence" from an alignment
- window or from the main desktop "File" menu. In the popup window
- which appears, select PDB as the database and enter your known PDB id. If
- you know which chain you wish to retrieve, append the chain id after a colon
- eg 1GAQ:B
-
-Note 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.
-To see a particular structure, right click on a sequence name and from the
- popup menu select "Sequence -> View PDB Entry".
-The PDB Structure viewer will perform a pairwise alignment of your sequence
- and each PDB chain sequence. To view the results of the mapping, select "File
- -> View Mapping" from the structure viewer window.
-Moving the mouse over the structure will highlight the residue in the alignment
- window, and vice versa.
-"Colour by Charge/Cysteine" will colour all Aspartate and Glutamate
- residues red, Lysine and Arginine will be blue and Cysteine residues will be
- coloured yellow.
-Tips for Viewing Structures
-
- - Colour By Sequence follows the exact colours of the alignment window, including
- sequence features. Thus you can easily view Uniprot sequence features, eg
- helix or metal binding sites on both the alignment and structure viewer.
- - Deselect Colours->Show All Chains in order to view only the mapped chain.
-
- - Use Wireframe, without depthcue, and without Z Buffering in order to accelerate
- the rendering of the structure.
- - You can save an image of your structure as a PNG or EPS file.
- - Use the cursor keys Up and Down arrow to zoom in and zoom out
-
-
-
+
+
+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
+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.
+
+