From: tcofoegbu Date: Tue, 21 Apr 2015 15:42:28 +0000 (+0100) Subject: JAL-1667_1668 Updated documentation X-Git-Tag: Jalview_2_9~56^2~1^2~1 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4f9d1e48b9d0231de697b36971311e4908490762 JAL-1667_1668 Updated documentation --- diff --git a/help/html/features/schooser_enter-id.png b/help/html/features/schooser_enter-id.png new file mode 100644 index 0000000..dc5aa93 Binary files /dev/null and b/help/html/features/schooser_enter-id.png differ diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index b276897..830c801 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -28,36 +28,82 @@ Structure Chooser

- The Structure Chooser panel was added in Jalview 2.8.3. It - introduced a smarter technique for selecting PDB structures to view in - Jalview by quering readily available meta-data of the structures. Some of the main features it provides are listed below: + The Structure Chooser interface provides a smart technique for + selecting PDB structures to view in Jalview by querying readily + available meta-data of structures. The Interface can be invoked by selecting + the + "View Structure" option from a sequence's + pop-up menu. Some of the main + features it provides are listed below: Additionally, the Structure Chooser retains the following contemporary - feature of Jalview: + features of Jalview: -

- -
- - Auto-Selection of Structures - +
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. +

+ +

+ Manual selection/association of PDB files with Sequences +

+

To manually associate PDB files with a sequence, select any of + the follwing options listed below from the drop-down menu in the + interface: +

+ +

+ The Structure Chooser panel was introduced in Jalview 2.x.x. + +

\ No newline at end of file diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index bece211..506beef 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -29,18 +29,17 @@ 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. + sequence's pop-up menu to invoke the Structure Chooser interface.
      -
    • If one or more structures exists for the given sequence, the 'Structure Chooser' +
    • 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' dialogue is opened with options for manual association of PDB structures.
      • +
    • However, if no structure was found, the Structure Chooser interface is opened with options for manual association of PDB structures.
    2. -
  2. Choose the structure to view from the presented structures - summary list. This can be done either manually by clicking directly - on the desired structure from the list, or automatically by - using the filter combo-box which enables filtering on certain - criteria like quality, resolution, etc. The best structure for the chosen criteria is automatically selected by the filtration process.
    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. When the desired structure(s) have been selected, they can be viewed by clicking the "View" button below the summary list.
    5. @@ -101,27 +100,7 @@ structure is selected, one of the following will happen:

  5. See the Jmol and Chimera PDB viewer help pages for more information about the display.
    6. -

    Associating PDB files with Sequences

    -

    Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the "View Structure" option is selected - from a sequence's pop-up menu. Jalview uses the sequence's ID to query the PDB Rest API, provided by the - EBI to discover PDB ids associated with the sequence.

    - -

    Manual association of PDB files with Sequences

    -

    To manually associate PDB files with a sequence, right click on a sequence -ID and select the "View Structure" option, this opens the 'Structure Chooser' dialogue. Then pick any of the follwing options listed below from the drop-down menu in the 'Structure Chooser' panel to proceed with manual association: -

    - -Note: The drop-down menu in the 'Structure Chooser' panel may contain other options employed for filtering structures when one or more structures are auto-discovered.

    Importing PDB Entries or files in PDB format
    You can retrieve sequences from the PDB using the