From bb5c8d98be1c4965b1a43b97f05b07e9ceb10343 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 28 Nov 2006 10:46:22 +0000 Subject: [PATCH] 2.2 documentation --- help/html/features/hiddenRegions.html | 10 ++++-- help/html/features/multipleViews.html | 12 ++++--- help/html/features/pdbviewer.html | 7 ++-- help/html/features/viewingpdbs.html | 64 ++++++++++++++++----------------- 4 files changed, 50 insertions(+), 43 deletions(-) diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html index 66413d9..3f7b599 100644 --- a/help/html/features/hiddenRegions.html +++ b/help/html/features/hiddenRegions.html @@ -24,9 +24,13 @@ the sequences in that group.
The hidden representative sequences will not be used in any calculations or web service alignments (nb. this may change in the future).
-Warning:The representative sequence groups feature is -not fully implemented in the jalview 2.2 release, following the -introduction of Multiple views.

+
Warning:hidden +representative sequence groups are only partly implemented in the +jalview 2.2 release. When a hidden representative group is created in +one alignment view, it will be propagated to all other views. Similarly, +revealing the represented sequences in one view will reveal them in all +other views. This will be resolved in a future Jalview release.
+

Hiding Columns
To hide selected columns in an alignment, use the "View -> Hide -> Selected Columns" menu item, or right click within diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html index 36bda32..7b17d06 100644 --- a/help/html/features/multipleViews.html +++ b/help/html/features/multipleViews.html @@ -40,11 +40,13 @@ to any or all other views.

calculation on a particular view may also be associated with other views, using the PCA Viewer's "View→Associate Nodes" submenu.

-

A PDB Structure Viewer opened on a -structure associated with a sequence in a particular view will also, by -default, only be associated with the sequence as it is displayed in that -view. The "View→Associate View" submenu allows the -association of alternative views.

+

Currently, a PDB Structure Viewer +opened on a structure associated with a sequence in a particular view +will only be associated with the seuqence as displayed in that view.
This +will be resolved in a future release

Multiple Views were introduced in Jalview 2.2

diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index 97471a2..9e1e6e5 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -8,7 +8,8 @@ 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.

+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 @@ -121,9 +122,9 @@ and alpha carbon location.

  • 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.
    • -
  • Associate View
    +
    • diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index ef222b1..4b4920d 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,32 +1,32 @@ - -PDB Viewing - -

    Viewing PDB Structures

    -

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

    -

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

    - -

    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).

    -

    For help on viewing and colouring structures see the PDB Viewer help page.

    - - + +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 "Sequence→View PDB + entry:" entry from the sequence's pop-up menu.

    +

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

    + +

    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).

    +

    See the PDB Viewer help page for more information.

    + + -- 1.7.10.2