From fa35c4093e7b2ff0d572a59b253a3d9f2597bc69 Mon Sep 17 00:00:00 2001 From: James Procter Date: Thu, 2 Nov 2023 16:29:19 +0000 Subject: [PATCH 1/1] JAL-4090 JAL-4147 documentation for revised sequence associated annotation display and pop-up menu --- help/help/html/features/xsspannotation.html | 18 ++++++++++-------- help/markdown/releases/release-2_11_3_0.md | 4 +++- 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/help/help/html/features/xsspannotation.html b/help/help/html/features/xsspannotation.html index 870b005..5f33dfe 100644 --- a/help/help/html/features/xsspannotation.html +++ b/help/help/html/features/xsspannotation.html @@ -29,8 +29,9 @@

Jalview can process PDB data associated with sequences to display values extracted from the Temperature Factor column for - corresponding sites, and secondary structure from DSSP or RNAView - (as appropriate). + corresponding sites, and secondary structure from DSSP. For computationally determined structures, jalview will show + model quality data encoded in the temperature factor column as AlphaFold Reliability (PLDDT) or Model + Quality as appropriate.

Extracting data from PDB files
Annotation is @@ -43,20 +44,21 @@ the Add Reference Annotation in the Selection and Sequence ID sub-menus of the Sequence ID Panel's popup menu.
Please note:Protein structures - are analysed in situ, but Jalview employs a web service to - process RNA structures which can cause long delays if your internet - connection is slow. + are analysed in situ.

The Annotations alignment menu provides settings useful for controlling the - display of secondary structure annotation. -

+ display of sequence-associated annotation. To compare several tracks from different structures for one or more + sequences, use 'sort by label' - which will also display PDB and Chain IDs for secondary structure and temperature + factor/quality annotation tracks for easier identification. +

Shading sequences by associated structure annotation
The annotation colouring dialog (opened by the Colour→By - Annotation option) allows sequences with associated secondary + Annotation option) or by right-clicking a particular annotation tracks's label allows sequences with + associated secondary structure data to be shaded according to secondary structure type. Once the dialog is opened, select the Per Sequence option and then choose Secondary structure from the dropdown menu.
When diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md index f3888cf..969c53f 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -21,7 +21,7 @@ channel: "release" - Command line options and configurable bitmap export preferences for height, width and scale factor - Show or hide ligands in a Jmol structure view via View Ligands submenu -### Improved support for working with computationally determined models +### Improved support for working with structures and computationally determined models - Alphafold red/orange/yellow/green colourscheme for structures - Interactive picking of low pAE score regions - contact matrix datatype in Jalview @@ -35,6 +35,8 @@ channel: "release" - Store/Restore PAE data and visualisation settings from Jalview Project - Store and restore adjustable ID margin and annotation panel height in Jalview projects - Multiple residue sidechain highlighting in structure viewers from PAE mouseovers +- Per-structure and chain shown when annotation shown sorted by label enabling secondary structure and temperature factor scores from different chains and structures for the same sequence to be visually compared. + ### Jalview on the command line - New command line argument framework allowing flexible batch processing, import of structures, pae matrices and other sequence associated data, and alignment and structure figure generation. -- 1.7.10.2