From f850089f8bc67403194f4a1a3b793a46dbb4224a Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 9 Dec 2005 18:47:23 +0000 Subject: [PATCH] Rearranged 'What's new' and debugged/verified the sequence fetcher and pdbviewer/viewingpdbs entries. --- help/help.jhm | 1 + help/helpTOC.xml | 2 +- help/html/features/pdbviewer.html | 120 ++++++++++++++++++++++++++----------- help/html/features/seqfetch.html | 4 +- help/html/menus/popupMenu.html | 12 ++-- 5 files changed, 96 insertions(+), 43 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index d9f255d..bb3990f 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -15,6 +15,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 752b4eb..77f105e 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -5,7 +5,7 @@ - + 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.

+

+ + + + + + + +
ActionWindowsUnixMac/OSX
Select/
Deselect
Residue		Left ClickLeft +ClickClick
Rotate ViewLeft Click and DragLeft Click and +DragClick and Drag
Roll ViewRight Click and dragRight Click and +DragTODO
Move OriginMiddle-Button and +DragMiddle-Button and DragTODO
Zoom InUp ArrowUp ArrowUp +Arrow
Zoom OutDown ArrowDown ArrowDown 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
    • -
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 2833770..fe1cfb8 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -9,14 +9,14 @@ WSDBFetch service provided by the European Bioinformatics Institute.

alignment, or opened via the "File" menu of an existing alignment to import additional sequences.

-

Select the database you want to retrieve sequences from, and enter a +

Select the database you want to retrieve sequences from, and enter the database id (or a semi-colon separated list of several ids) in the text box. Finally, press OK to initiate the retrieval.

If you are retrieving sequences from the PDB, you can retrieve specific chains by appending a colon and the chain id to the PDB id. For example :

 1GAQ:A

-

If you use the sequence fetcher in work for publication, then please cite:

+

If you use the sequence fetcher in work for publication, please cite:

Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
SOAP-based services provided by the European Bioinformatics Institute.
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 94ffb3c..fd65178 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -48,11 +48,15 @@ your edit.

  • View PDB Structure
    -     In the current version you will first need to select "View - -> Sequence Features" before associating a PDB file with a sequence. -
    + If the sequence has a PDB file associated with it Jalview will display - a 3D interactive viewer of the file.
    • + a 3D interactive viewer of the file.
    +This entry is only present if the sequence has an + associated PDB structure. + If you can't see this entry for your sequence, and the sequence name + is a uniprot identifier, then try enabling the "View + -> Sequence Features" and opening the popup menu again.     +
  • Link
    -- 1.7.10.2