From c4bd086791a762332a817543ed4de1a6d06b72bf Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 8 May 2007 13:48:40 +0000 Subject: [PATCH] added jmol documentation --- help/help.jhm | 2 + help/helpTOC.xml | 6 +- help/html/features/jmol.html | 150 +++++++++++++++++++++++++++++++++++ help/html/features/pdbviewer.html | 6 ++ help/html/features/viewingpdbs.html | 93 ++++++++++++---------- 5 files changed, 214 insertions(+), 43 deletions(-) create mode 100644 help/html/features/jmol.html diff --git a/help/help.jhm b/help/help.jhm index bb3b49f..c0a9d68 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -24,6 +24,8 @@ + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 04bfc7e..4338d36 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -4,6 +4,7 @@ + @@ -13,7 +14,6 @@ - @@ -64,6 +64,10 @@ + + + + diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html new file mode 100644 index 0000000..3402add --- /dev/null +++ b/help/html/features/jmol.html @@ -0,0 +1,150 @@ + + +The Jmol PDB Viewer + + +

The Jmol PDB Viewer +

The 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. +

Since Jalview 2.3, Jmol +has been integrated into Jalview. It is automatically used by the +application, and should also run in the applet in all latest web +browsers. If jmol is not available, then the original internal pdb viewer will be used as a fallback. +

+

Controls

+

The structure is by default rendered as a ribbon diagram. Moving the +mouse over the structure brings up tooltips giving the residue name, +PDB residue number and chain code, atom name and number +([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue +in any associated sequences, then this will be highlighted in each +one's alignment window. The converse also occurs - moving the mouse +over an associated residue in an alignment window highlights the associated +atoms in the displayed structures.

+

Selecting a residue highlights its associated sequence residue +and alpha carbon location. Double clicking an atom allows distances to +be measured from it to any other atom in the structure.

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ActionWindowsUnixMac/OSX
Rotate ViewLeft Click and DragLeft Click and DragClick and Drag
ZoomShift + Left Click
drag mouse up or down		Shift + Left Click
or middle button
drag + mouse up or down		Left-Alt + Click and drag mouse up or down
Select/
+ Deselect
+ Residue		Left ClickLeft ClickClick
Roll ViewShift + Left Click
drag mouse to left or + right		Shift + Left Click
or middle button
drag mouse to left or right		Left-Alt + Click and drag mouse to left or right
Move OriginShift+Control+Left Click
or Middle Button
+ + Drag		Middle-Button
and
drag		Shift+Control+Left Click
or Middle Button
+ and drag
Jmol MenuRight-ClickRight-ClickApple-Click
+

+

The window has four menus: +

    +
  • File
    +     +
      +
    • Save As
      +       Save the displayed PDB File, or 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.
      • +
    +
    • +
  • View +
      +
    • Show Chains
      Select which of the PDB + file's chains are to be displayed. +
      • +
    +
  • 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.
      • +
    +
    • +
  • Help
    • Jmol Help
      Access the Jmol Help + documentation in a new browser window. +
      • +
    +
+

+

Functionality provided by Jmol +

The Jmol menu provides access to a number of features for +controlling the colour and display of molecules, adding measurements and +labels, plotting surfaces, and display animation. The 'Set Picking' +menu controls the behaviour of single and double mouse clicking on the +structure.

+

The state of each Jmol display is stored within jalview archives using Jmol's own state +storage format. This means that any Jmol visualization effects that +you add beyond those provided by Jalview will be able to be stored and +recovered along with the displayed alignments in Jalview. +

More Information +

Jmol is a sophisticated program in its own right, with its own +command console and scripting language. Only the essentials have been +described here - the interested reader is referred to +Jmol's own comprehensive +online documenation.

+ + diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index 9e1e6e5..fc69f9b 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -3,6 +3,12 @@ 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 diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 842ad3e..c3bdc6b 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,42 +1,51 @@ - -PDB Viewing - -

Viewing PDB Structures

-

Jalview has a simple 3D structure viewer which - can visualize polypeptide backbone structures associated with a sequence in - a particular alignment view. It is accessed via the "Strucutre→View - PDB entry:" entry from the sequence's pop-up menu.

-

Since Jalview 2.3, Jmol has been integrated into the application and will also - run in the applet in all latest web browsers. For more help using Jmol, see - http://jmol.sourceforge.net/docs/JmolUserGuide/ -

-

To associate PDB files with a sequence, right click on a sequence ID and select - "Structure→ Associate Structure with Sequence", - and one of the submenus:

-
    -
  • From File - You can load a PDB file from the local machine or network and - associate it with the selected sequence. PDB files associated in this way - will also be saved in the Jalview Archive file.
    -
    • -
  • Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch - the PDB file with the entered Id.
    -
    • -
  • Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover - PDB ids for all the sequences in the alignment which have valid Uniprot names - / accession ids.
    • -
-

Note: You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with this - service are automatically associated with their source database entry. For PDB - sequences, simply select PDB as the database and enter your known PDB id (appended - with ':' and a chain code, if desired).

-

Sequences which have PDB File associations are annotated with sequence features - from the group 'PDBFile' giving the corresponding PDB Residue Number for each - mapped residue in the seuqence. The display of these features is controlled through - the "View→Sequence Features" menu item and the - Feature Settings dialog box.

-

See the PDB Viewer help page for more information.

- - + +PDB Viewing + +

Viewing PDB Structures

+

Jalview can view protein structures associated with a sequence via the "Structure→View + PDB entry:" entries from a sequence's pop-up menu. This will open an + interactive display of the structure in a new window, or prompt you + to associate the sequence with an existing view of the selected + structure. See the Jmol PDB viewer help page + for more information about the display. +

+

To associate PDB files with a sequence, right click on a sequence ID and select + "Structure→ Associate Structure with Sequence", + and one of the submenus:

+
    +
  • From File - You can load a PDB file from the local machine or network and + associate it with the selected sequence. PDB files associated in this way + will also be saved in the Jalview Archive file.
    +
    • +
  • Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch + the PDB file with the entered Id.
    +
    • +
  • Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover + PDB ids for all the sequences in the alignment which have valid Uniprot names + / accession ids.
    • +
+

Importing PDB Entries or files in PDB format
+You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with this + service are automatically associated with their source database entry. For PDB + sequences, simply select PDB as the database and enter your known PDB id (appended + with ':' and a chain code, if desired). +
Jalview will also read PDB files directly. Simply load in the file +as you would an alignment file. The sequences of any peptide chains +will be extracted from the file and viewed in the alignment window. +
Note for jalview applet users: due to the applet security +constraints, PDB Files can currently only be imported by cut and paste +of the PDB file text into the text box opened by the 'From File' entry +of the structure menu.

+

Viewing the PDB Residue Numbering
+Sequences which have PDB entry or PDB file associations are annotated +with sequence features from a group named with the associated PDB +accession number or file name. Each feature gives the corresponding +PDB Residue Number for each mapped residue in the seuqence. The +display of these features is controlled through the +"View→Sequence Features" menu item +and the Feature Settings dialog +box.

+ + -- 1.7.10.2