From: Ben Soares Date: Fri, 5 Nov 2021 10:14:12 +0000 (+0000) Subject: JAL-3746 Updated help docs for 3D-Beacons. Added and altered images and text. X-Git-Tag: Release_2_11_2_0~24^2~3 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=e685afadb350fda906f1e360dfa30ad2cb476a2a;p=jalview.git JAL-3746 Updated help docs for 3D-Beacons. Added and altered images and text. --- diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index a72f5ac..5479291 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -131,7 +131,7 @@ - + diff --git a/help/help/html/features/3dbeacons_button.png b/help/help/html/features/3dbeacons_button.png new file mode 100644 index 0000000..2dae1f6 Binary files /dev/null and b/help/help/html/features/3dbeacons_button.png differ diff --git a/help/help/html/features/3dbeacons_structurechooser.png b/help/help/html/features/3dbeacons_structurechooser.png new file mode 100644 index 0000000..cd7fdab Binary files /dev/null and b/help/help/html/features/3dbeacons_structurechooser.png differ diff --git a/help/help/html/features/3dstructuredata_popupmenu.png b/help/help/html/features/3dstructuredata_popupmenu.png new file mode 100644 index 0000000..e5de4ca Binary files /dev/null and b/help/help/html/features/3dstructuredata_popupmenu.png differ diff --git a/help/help/html/features/schooser_main.png b/help/help/html/features/schooser_main.png index ca793fd..07a1a3c 100644 Binary files a/help/help/html/features/schooser_main.png and b/help/help/html/features/schooser_main.png differ diff --git a/help/help/html/features/schooser_viewbutton.png b/help/help/html/features/schooser_viewbutton.png new file mode 100644 index 0000000..f14481e Binary files /dev/null and b/help/help/html/features/schooser_viewbutton.png differ diff --git a/help/help/html/features/selectfetchdb.gif b/help/help/html/features/selectfetchdb.gif index de0a7e6..6103b31 100644 Binary files a/help/help/html/features/selectfetchdb.gif and b/help/help/html/features/selectfetchdb.gif differ diff --git a/help/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html index 4e9a75f..7d4a389 100755 --- a/help/help/html/features/seqfetch.html +++ b/help/help/html/features/seqfetch.html @@ -38,7 +38,7 @@ the database you want to retrieve sequences from the database chooser.

Database selection dialog for fetching sequences (introduced in Jalview 2.8)

The databases are shown as a tree, and ordered alphabetically; @@ -69,7 +69,10 @@ accession ids (as a semi-colon separated list), or press the "Example" button to paste the example accession for the currently selected database into the retrieval box. Finally, press - "OK" to initiate the retrieval. + "OK" to initiate the retrieval. +
+ For the PDB and UniProt sequence fetchers, choose the "Retrieve IDs" tab + to search for accession ids.

If you use the Sequence Fetcher, please remember to cite the diff --git a/help/help/html/features/seqfetcher.gif b/help/help/html/features/seqfetcher.gif index 03ddd79..6b9ff21 100644 Binary files a/help/help/html/features/seqfetcher.gif and b/help/help/html/features/seqfetcher.gif differ diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html index 785c429..11cad6b 100644 --- a/help/help/html/features/structurechooser.html +++ b/help/help/html/features/structurechooser.html @@ -32,8 +32,11 @@ 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 + Structure Data..." option from the Sequence ID panel's + pop-up menu.
+ +
+ The dialog provides:

initiate a search + of the 3D-Beacons Network

Viewing existing structures for your sequences @@ -86,7 +92,7 @@

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 + structure data, the 'PDBe 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 @@ -103,7 +109,39 @@
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).

+ PDB records will be shown (see below). + +

+ 3D-Beacons Network Search +

+ To initiate a search of the 3D-Beacons Network—which searches + across experimentally determined and predicted structure models from + several resources including PDBe, AlphaFold DB, SWISS-MODEL, PED, SASDB, Genome3D and + PDBe-KB—click on the 3D-Beacons Search button at the top of the + Structure Chooser window. +
+ +
+ The 3D-Beacons Network search requires UniProt references and Jalview will ask + to attempt to fetch these references for the selected sequences. + UniProt references might not always be found in which case you can revert to the PDB + search. +
+ +
+ If structures are found through the 3D-Beacons network you can filter which structures + are shown using the drop-down filter at the top of the Structure Chooser window. +
+ You can view information about each related model, such as the resource providing + each model, in the columns displayed. You can sort the list of models by clicking on + column headings. +
+ Select and view the structures in the usual way using the open structure options at + the bottom of the Structure Chooser window. +

Exploration of meta-data for available structures

Information on each structure available is displayed in columns @@ -135,4 +173,4 @@ 2.9.

- Discovering and Viewing PDB Structures + Discovering and Viewing PDB and 3D-Beacons structures

Structure Chooser

If one or more structures exists for the given +
If one or more structures exist in the PDB for the given sequence, the Structure Chooser dialog will open with them listed in the results pane. @@ -43,9 +43,17 @@ href="structurechooser.html">Structure Chooser interface will present options for manual association of PDB structures.
+ Since Jalview 2.11.2 you can also search the 3D-Beacons Network + for structures. The 3D-Beacons Network acts as a one-stop shop for protein + structures by combining and standardising data from several providers. + See 3D-Beacons Search for + instructions. +

Selecting Structures
You can select +
Selecting PDB Structures
+ If one or more structures have been found from the PDB, you can select the structures that you want to open and view by selecting them with the mouse and keyboard.
By default, if structures were discovered, then some will already be selected according to the @@ -79,7 +87,8 @@ Structure Viewers in the Jalview Desktop
The Jmol viewer has been included since Jalview 2.3. Jalview 2.8.2 included support for Chimera, - provided it is installed and can be launched by Jalview. The default + provided it is installed and can be launched by Jalview. ChimeraX and PyMOL + support is included from Jalview 2.11.2. The default viewer can be configured in the Structure tab in the Tools→Preferences dialog box. @@ -90,12 +99,14 @@ for more information.

-
Controlling where the new structures will be shown +
+
The Structure Chooser offers several options - for viewing a structure.
New View will open a new + for viewing a structure.
+ The Open new structure view button will open a new structure viewer for the selected structures, but if there are views already open, you can select which one to use, and press the Add button. Jalview can automatically superimpose new structures based