PDB Viewer

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=bd240ea4bd2b9d4ea492dfdfd309c40296771af2;hb=3fb85e9272c55b49583d558ca9c44babcf1b3a0b;hp=a7e2c108442a85413d4919c35eaf33ed754f1d0d;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index a7e2c10..bd240ea 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,45 +1,93 @@ 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.

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:

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
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. +
-
Note the applet can only load PDB files by copying and pasting the text into +
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.

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

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