From: Jim Procter Date: Tue, 1 May 2018 09:29:19 +0000 (+0100) Subject: JAL-2944 revised docs and structure chooser screen shots X-Git-Tag: Release_2_10_4~29 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=978ff69a2fa5b918f8c39c10c0536f2872c8df27;p=jalview.git JAL-2944 revised docs and structure chooser screen shots --- diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index 0cd6168..ac2489b 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -61,16 +61,10 @@

-->

Superposing structures based on - their aligned sequences
If several structures are - available on the alignment, you may add additional structures to an - existing Jmol view by selecting their entry in the appropriate - pop-up menu. Jalview will ask you if you wish to add the structure - to the existing alignment, and if you do, it will import and - superimpose the new PDB file using the corresponding positions from - the alignment. If the alignment is subsequently edited, you can use - the Jmol→Align menu option from - the menu bar of the structure view window to superpose the - structures using the updated alignment.
Sequence + their aligned sequences
If several structures are shown + in a view, you can superimpose them using the corresponding + positions from the alignment via the Jmol→Align + menu option from the menu bar of the structure view window.
Sequence based structure superposition was added in Jalview 2.6

diff --git a/help/html/features/schooser_enter-id.png b/help/html/features/schooser_enter-id.png index f551c50..4af0d53 100644 Binary files a/help/html/features/schooser_enter-id.png and b/help/html/features/schooser_enter-id.png differ diff --git a/help/html/features/schooser_main.png b/help/html/features/schooser_main.png index ab69427..ca793fd 100644 Binary files a/help/html/features/schooser_main.png and b/help/html/features/schooser_main.png differ diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index fc71826..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 + 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 option from the Sequence ID panel's pop-up menu. The dialog provides:

@@ -49,11 +49,16 @@

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 - button will import them into Add button will import them a new or existing - structure view. + 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 @@ -89,17 +94,16 @@ 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. If no structures were - auto-discovered, options for manually associating PDB records will be shown (see 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 @@ -109,7 +113,7 @@ Columns' tab and tick the columns which you want to see.

+ style="width: 464px; height: 173px;">
Manual selection/association of PDB files with Sequences diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 45d979f..b1ad4ba 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -82,6 +82,7 @@ provided it is installed and can be launched by Jalview. The default viewer can be configured in the Structure tab in the Tools→Preferences dialog box. +

Structure data imported into Jalview can also be processed to display secondary structure and temperature factor annotation. See @@ -89,44 +90,30 @@ for more information.

- After pressing the - 'View' button in the Structure Chooser
The behaviour of - the 'View' button depends on the number of structures selected, and - whether structure views already exist for the selected structures or - aligned sequences. +
Controlling where the new structures + will be shown +
The Structure Chooser offers several options + for viewing a structure.
New View 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 + on the linked alignments - but if this is not desirable, simple + un-tick the Superpose Structures checkbox. +

-

If multiple structures are selected, then Jalview will always - create a new structure view. The selected structures will be - imported into this view, and superposed with the matched positions - from the aligned sequences. A message in the structure viewer's - status bar will be shown if not enough aligned columns were - available to perform a superposition.

- If a single PDB structure is selected, one of the - following will happen: + Superposing structures
Jalview superposes structures using + the visible portions of any associated sequence alignments. A + message in the structure viewer's status bar will be shown if not + enough aligned columns were available to perform a superposition.

- - - +

+ See the Jmol + and Chimera help pages for + more information about their capabilities.

+

Retrieving sequences from the PDB
You can