From a7a1a8a1230cffc66285053d72e50c84f0a7faa2 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 19 Sep 2016 18:57:05 +0100 Subject: [PATCH] JAL-2189 JAL-2002 revised the structure chooser documentation --- help/html/features/structurechooser.html | 127 +++++++++++++++--------------- help/html/releases.html | 2 +- 2 files changed, 63 insertions(+), 66 deletions(-) diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index f5f5916..c9600bb 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -28,57 +28,51 @@ Structure Chooser

- 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 - "3D Structure Data.." option from a sequence's - pop-up menu. Some of the main - features it provides are listed below: +

+ 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 pop-up menu. The dialog + provides: +

- Additionally, the Structure Chooser retains the following contemporary - features of Jalview: - - - Associating PDB files with Sequences -
Discovery/Association of PDB entries to a sequence now - happens automatically during the initialisation of the Structure - Chooser Interface. Jalview uses the sequence's ID to query the PDB - Rest API provided by the EBI to discover PDB Ids associated with the - sequence. - -
-
- Configuring displayed meta-data for Structures -
To configure the visible meta-data displayed for the - discovered structures, click the 'Configure Displayed Columns' tab, - then tick the options which you intend to make visible. - -
-
- Auto-selection of best Structures -
Jalview can automatically filter and select the best - structures using various metric categories avaialble from the - meta-data of the structures. To perform this simply select any of the - following options from the drop-down menu in the Structure Chooser - interface: Best UniProt coverage, Higest Resolution, Best Quality, - Highest Protein Chain etc. When the 'Invert' option is selected, - Jalview returns an inverse result for the current selected option in - the drop-down menu. +

+ 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 + associated with the sequence. It does this based on the sequence's + ID string, and any other associated database IDs.

+

+ 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.

+

+ 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).

@@ -92,32 +86,35 @@ 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. +

+ style="width: 464px; height: 369px;"> +

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: +

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 diff --git a/help/html/releases.html b/help/html/releases.html index cd8dae0..d7e036f 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -62,7 +62,6 @@

    • -
  • Updated download sites used for Rfam and Pfam sources to xfam.org
  • Disabled Rfam(Full) in the sequence fetcher
  • Show residue labels in Chimera when mousing over sequences in Jalview
    • @@ -108,6 +107,7 @@
  • Columns are suddenly selected in other alignments and views when revealing hidden columns
  • Hide columns not mirrored in complement view in a cDNA/Protein splitframe
  • Cannot save/restore representative sequence from project when only one sequence is represented
    • +
  • Disabled 'Best Uniprot Coverage' option in Structure Chooser
    • -- 1.7.10.2