X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=785c42978170887d5250aaa472945b1b8c421cb5;hb=e1cb1f4ff4ae05504c806d99395358629c807956;hp=f5f5916ed98d0517676a7e0b9807e1137fb982d4;hpb=d0771875f23ab994c4f85fb6cd604378768df10e;p=jalview.git diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index f5f5916..785c429 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -25,98 +25,109 @@

- Structure Chooser + Structure Chooser Dialog Box

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

Automatic discovery, retrieval and association of PDB - entries for an alignment's sequences
Visualisation of discovered structures' meta-data
Ability to configure the meta-data entries to visualise
Auto-selection of the best structure via filtering by the - available metric parameters in the meta-data (i.e. resolution, - quality etc).
Selection of multiple structures in a single operation

- Additionally, the Structure Chooser retains the following contemporary - features of Jalview: -

Manual association of PDB entries via entering the PDB Id - or From File
Ability to view cached PDB entries
Exploration of meta-data for available 3D structures
Automatic selection of the 'best structure' to display for + each sequence
Manual association of PDB entries by entering a PDB Id
Association of structure data from a local file (in mmCIF + or PDB format)

- - - 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. +

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

+ 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. +

+ Selection of the best structure for each sequence +

Jalview can automatically select the best structures according + 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 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:

From File - You can load a PDB file from - the local machine or network and associate it with the selected - sequence. PDB files associated in this way will also be saved in - the Jalview Archive file.
Enter PDB Id - Jalview will use the PDB - Rest API, provided by the EBI, to fetch the PDB file with the - entered Id.
Cached PDB Entries - You can view PDB - structures which have previously been downloaded/viewed using this - option. Jalview caches previously downloaded PDB entries in the - computer memory. However, if the project is saved before exiting - Jalview, Jalview will serialize the cached entries to the file - system.
From File - allows you to load a PDB file + from the local machine or network and associate it with the + selected sequence. PDB files associated in this way will also be + saved in the Jalview Archive file.
Enter PDB Id - allows you specify a PDB ID + for your sequence. The PDB Rest API, provided by EMBL-EBI, is used + to validate and fetch structure data.