From 08135222cb5e0df30da1d9fb548fccbc7d8ef3fd Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 18 Oct 2016 15:20:06 +0100 Subject: [PATCH] =?utf8?q?JAL-2039=20rejig=20instructions=20for=20Structure=20?= =?utf8?q?Chooser=20and=20clarify=20what=20happens=20after=20=E2=80=98View=E2?= =?utf8?q?=80=99=20is=20pressed?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/html/features/structurechooser.html | 73 ++++++++++++++++++------------ help/html/features/viewingpdbs.html | 40 +++++++++++----- 2 files changed, 71 insertions(+), 42 deletions(-) diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index daa1ac3..fc71826 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -31,7 +31,7 @@

The Structure Chooser interface allows you to interactively select which PDB structures to view for the currently selected set of - sequences. It's opened by selecting the "3D + sequences. It is opened by selecting the "3D Structure Data.." option from the Sequence ID panel's pop-up menu. The dialog provides: @@ -46,33 +46,47 @@

  • Association of structure data from a local file (in mmCIF or PDB format)
    • - +

    + Selecting and Viewing Structures +

    +

    + Once one or more structures have been selected, pressing the View + button will import them into a new or existing + structure view. +

    Automated discovery of structure data

    -

    After selecting "3D Structure Data ..", Jalview queries the PDB - via the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB ids +

    + After selecting "3D Structure Data ..", Jalview queries the PDB via + the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB IDs associated with the sequence. It does this based on the sequence's - ID string, and any other associated database IDs.

    + ID string, and any other associated database IDs.
    +

    - Exploration of meta-data for available structures + Viewing existing + structures for your sequences +

    +

    + If you have already loaded 3D structure data for the selected + sequences, the structure chooser will first open with the Cached + Structures View. This view shows associations between each + sequence, and chains for 3D structure files already in memory. If + you want to download additional structures, select one of the other + options from the drop down menu.

    -

    Information on each structure available is displayed in columns - in the dialog box. By default, only the title, resolution and PDB - identifier are shown, but many more are provided by the PDBe. To - configure which ones are displayed, select the 'Configure Displayed - Columns' tab and tick the columns which you want to see.

    Selection of the best structure for each sequence

    Jalview can automatically select the best structures according - to meta-data provided by the PDB. By default, the 'Best Quality' - structure for each sequence will be selected, but clicking on the - drop down menu allows other criteria to be chosen, including - Resolution (only defined for X-Ray structures), Highest Protein - Chain etc. When 'Invert' is selected, structures are selected in - reverse order for the current criteria (e.g. worst quality rather - than best).

    + to meta-data provided by the PDB. For alignments with no existing + structure data, the 'Best Quality' structure for each sequence will + by default be selected, but clicking on the drop down menu allows + other criteria to be chosen, including Resolution (only defined for + X-Ray structures), Highest Protein Chain etc. When 'Invert' is + selected, structures are selected in reverse order for the current + criteria (e.g. worst quality rather than best).

    @@ -83,13 +97,20 @@

    -->
    The screenshot above shows the Structure Chooser interface along with the meta-data of auto-discovered structures for the - sample alignment. Note however that if no structures were - auto-discovered, a different interface for manual association will - be invoked as seen in the screenshot below. + sample alignment. If no structures were + auto-discovered, options for manually associating PDB records will be shown (see below). +

    + Exploration of meta-data for available structures +

    +

    Information on each structure available is displayed in columns + in the dialog box. By default, only the title, resolution and PDB + identifier are shown, but many more are provided by the PDBe. To + configure which ones are displayed, select the 'Configure Displayed + Columns' tab and tick the columns which you want to see.

    -

    +
    Manual selection/association of PDB files with Sequences

    @@ -104,14 +125,6 @@ for your sequence. The PDB Rest API, provided by EMBL-EBI, is used to validate and fetch structure data.
    -

    - Viewing existing structures for your sequences -

    -

    - If you have previously associated structure data on the alignment, - selecting Cached PDB Entries from the drop down - menu allows you to select these structures for display. -

    The Structure Chooser interface was introduced in Jalview diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 21caca1..f60da1a 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -53,11 +53,12 @@ 'highest resolution', simply choose another to pick structures in a different way.

  • To view selected structures, click the "View" button. @@ -68,9 +69,14 @@
  • SIFTS records will also be downloaded for mapping UniProt protein sequence data to PDB coordinates.
    • +
  • A new structure viewer will open, or you will be + prompted to add structures to existing viewers (see below for details). +
    • - +

    + Structure Viewers in the Jalview Desktop
    The Jmol viewer has been included since Jalview 2.3. Jalview 2.8.2 included support for @@ -84,10 +90,19 @@ the Annotation from Structure page for more information.

    -

    - If a single PDB structure is selected, one of the - following will happen: + After pressing the + 'View' button in the Structure Chooser
    The behaviour of + the 'View' button depends on the number of structures selected, and + whether structure views already exist for the selected structures or + aligned sequences. +

    +

    + If multiple structures are selected, then Jalview will always create + a new structure view. The selected structures will be imported into + this view, and superposed with the matched positions from the + aligned sequences.
    If a single PDB structure + is selected, one of the following will happen:

      @@ -96,9 +111,10 @@
    • If another structure is already shown for the current alignment, then you will be asked if you want to add and align this structure to the structure - in the existing view. (new feature in Jalview 2.6). -
      • + href="jmol.html#align"> to + the structure in the existing view. (new feature in Jalview + 2.6). +
    • If the structure is already shown, then you will be prompted to associate the sequence with an existing view of the -- 1.7.10.2