X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=785c42978170887d5250aaa472945b1b8c421cb5;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=c9600bb4bcb27933390c38771b33f84b97122dcc;hpb=a7a1a8a1230cffc66285053d72e50c84f0a7faa2;p=jalview.git diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index c9600bb..785c429 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -25,14 +25,14 @@

- Structure Chooser + Structure Chooser Dialog Box

- 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 - Structure Data.." option from the Sequence ID panel's "3D + Structure Data..." option from the Sequence ID panel's pop-up menu. The dialog provides:

@@ -46,58 +46,80 @@
  • Association of structure data from a local file (in mmCIF or PDB format)
    • - +

    + Selecting and Viewing Structures +

    +

    The drop-down menu offers different options for structure + discovery; the 'Cached' view is shown automatically if existing + structure data has been imported for the selected sequences, and if + none is available, the import PDB/mmCIF file options are shown.

    +

    + Once one or more structures have been selected, pressing the View + or Add button will import them a new or existing + structure view. When multiple views are available, use the + drop-down menu to pick the target viewer for the structures. +

    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).

    - + -
    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. - +
    The screenshot above shows the Structure Chooser displayed after + selecting all the sequences in the Jalview example project. 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.

    - -

    + style="width: 464px; height: 173px;"> +
    Manual selection/association of PDB files with Sequences

    To manually associate PDB files with a sequence, select 'From File', or 'Enter PDB Id' from the drop-down menu: -

    -

    - 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