From de255c8c87707a2cd2a2a15f5ad04ed10fe5846d Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 10 Sep 2015 02:53:26 +0100 Subject: [PATCH] JAL-1645 yet more documentation tweaks --- help/html/features/annotationsFormat.html | 57 +++++----- help/html/features/viewingpdbs.html | 59 ++++------ help/html/menus/alignmentMenu.html | 173 +++++++++++++++-------------- help/html/menus/alwannotationpanel.html | 2 +- help/html/menus/alwcalculate.html | 56 ++++++---- help/html/menus/alwselect.html | 13 ++- help/html/menus/alwview.html | 2 +- help/html/menus/popupMenu.html | 50 ++------- help/html/webServices/jnet.html | 19 +++- 9 files changed, 210 insertions(+), 221 deletions(-) diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index 60c9e23..4c8ad39 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -211,38 +211,43 @@ Group association is turned off for subsequent annotation rows by: 
GROUP_REF	ALIGNMENT

-

VIEW_SETREF, VIEW_HIDECOL and HIDE_INSERTIONS
-Since Jalview 2.9, the Annotations file has also supported the definition of reference sequences and hidden regions for an alignment view.

- -

- VIEW_SETREF marks the first sequence in the alignment, or - alternately, the one specified by the most recent SEQUENCE_REF - statement, as the reference - sequence for the alignment. -

-

- HIDE_INSERTIONSThis command hides all gapped positions in the - current target sequence. Any columns already hidden will be - re-displayed.
-
The current target sequence is either the one specified by - the most recent SEQUENCE_REF statement, the alignment's - reference sequence, or the first sequence in the alignment. -

-

- VIEW_HIDECOLS modifies the visibility of columns in the view. - The statement is followed by a single argument consisting of a comma - separated series of single integers or integer pairs (like 3-4). - These define columns (starting from the left-hand column 0) that - should be marked as hidden in the alignment view. -

+

+ VIEW_SETREF
Marks the first sequence in the alignment, + or alternately, the one specified by the most recent SEQUENCE_REF + statement, as the reference + sequence for the alignment. +

+

+ HIDE_INSERTIONS
This command hides all gapped + positions in the current target sequence. Any columns already hidden + will be re-displayed.

The current target sequence is + either the one specified by the most recent SEQUENCE_REF + statement, the alignment's reference sequence, or the first sequence + in the alignment. +

+

+ VIEW_HIDECOLS
Modifies the visibility of columns in + the view. The statement is followed by a single argument consisting + of a comma separated series of single integers or integer pairs + (like 3-4). These define columns (starting from the + left-hand column 0) that should be marked as hidden in the alignment + view. +

-
-

COMPATIBILITY NOTES
+

+

COMPATIBILITY NOTES
The interpretation of the COMBINE statement in Version 2.8.1 was refined so that only annotation line graphs with the given names ands the same SEQUENCE_REF and GROUP_REF scope are grouped.

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 3586083..6419525 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -28,23 +28,31 @@

Jalview can be used to view protein structures by following the steps below:
    -
  1. Select the "View Structure" option from a - sequence's pop-up menu to invoke the Structure Chooser interface. +
  2. Select the "3D Structure Data..." option from a + sequence's pop-up menu to open the Structure Chooser dialog box.
    • If one or more structures exists for the given sequence, the Structure Chooser - dialogue is opened with a list of the found structures meta-data.
      • -
    • However, if no structure was found, the Structure Chooser interface is opened with options for manual association of PDB structures.
      • + dialog will open with them listed in the results pane. +
    • However, if no structure was found, the Structure Chooser interface will present options for manual association of PDB structures.
    3. -
  3. Choose the structure to view from the discovered list. This can be done either manually by clicking directly - on the desired structure(s) in the list, or automatically by - using the drop-down menu on the interface to filter and auto-select the best structure based on certain - criteria like quality, resolution, etc.
    4. -
  4. When the desired structure(s) have been selected, they can be - viewed by clicking the "View" button below the summary list. -
    5. - -
+
  • Selecting Structures
    If structures + have been discovered, then some will already be selected according + to predefined selection criteria, such as structures with the + highest resolution. Use the drop down menu to select structures + according to different criteria, or, alternatively, choose + structures manually by selecting with the keyboard and mouse. +
    • +
  • To view selected structures, click the "View" + button. +
    • + The Jmol viewer has been included since Jalview @@ -59,29 +67,8 @@ href="xsspannotation.html">Annotation from Structure page for more information.

    - -

    If a single pdb +

    If a single PDB structure is selected, one of the following will happen:

    +
  • Select/Hide Columns by Annotation
    + Select or Hide columns in the alignment according to + secondary structure, labels and values shown in alignment + annotation rows.
    • + diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index e55a7f7..db1bfb1 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -34,7 +34,7 @@
  • Gather Views (G)
    Each view associated with the alignment will be displayed within its own tab on the current alignment window.
    • -
  • Show→(all Columns / Sequences / Sequences and Columns )
    +
  • Show→(all Columns / Sequences / Sequences and Columns)
    All hidden Columns / Sequences / Sequences and Columns will be revealed.
  • Hide→(all Columns / Sequences / Selected Region / All but Selected Region)
    Hides the currently selected Columns / Sequences / Region or everything but the selected Region.
    • diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 9d6a0c6..e7017f0 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -141,6 +141,10 @@ Annotations
    When enabled, copies any available alignment annotation for this sequence to the current view. +
  • Set as Reference or Unmark as Reference
    + Sets or unsets the reference sequence for the the alignment. +
    • +
  • Represent Group With (Sequence Id)
    All sequences in the current selection group will be hidden, apart from (Sequence Id). Any edits performed on the @@ -169,48 +173,10 @@ href="../features/varna.html">VARNA.
    • - - -
  • Hide Sequences
    Hides the +
  • Hide Insertions
    + Hides columns containing gaps in the current sequence or + selected region, and reveals columns not including gaps. +
  • Hide Sequences
    Hides the currently selected sequences in this alignment view.
    • diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index cf914d3..0f64115 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -24,12 +24,19 @@ JNet Secondary Structure Prediction -

    Secondary structure prediction methods attempts to infer the -likely secondary structure for a protein based on its amino acid -composition and similarity to sequences with known secondary structure. -The JNet method uses several different neural networks and decides on -the most likely prediction via a jury network.
    -

      +

      + Secondary structure prediction methods attempts to infer the likely + secondary structure for a protein based on its amino acid + composition and similarity to sequences with known secondary + structure. The most recent version of the method, JPred4, employs a + series of neural networks trained to predict different secondary + structure types from a sequence profile, and when necessary, employs + a jury network to identify the most likely secondary structure + prediction.

      • Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)
        +JPred4: a protein secondary structure prediction server
        +Nucleic Acids Research, Web Server issue (first published 15th April 2015)
        +http://dx.doi.org/10.1093/nar/gkv332 +
      • Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3 secondary structure prediction server Nucleic Acids Research 36 W197-W201
        • -- 1.7.10.2