From d829cd0ed80c9888a868a847d1e086671f6c6cc3 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Wed, 22 Jul 2015 09:55:42 +0100 Subject: [PATCH] JAL-1667 JAL-1668 JAL-1553 help docs update --- .../calculations/columnFilterByAnnotation.html | 36 +++++++++----------- help/html/features/pdbsequencefetcher.html | 16 ++++----- help/html/features/structurechooser.html | 10 +++--- 3 files changed, 29 insertions(+), 33 deletions(-) diff --git a/help/html/calculations/columnFilterByAnnotation.html b/help/html/calculations/columnFilterByAnnotation.html index a69e234..1ece1cc 100644 --- a/help/html/calculations/columnFilterByAnnotation.html +++ b/help/html/calculations/columnFilterByAnnotation.html @@ -27,24 +27,22 @@

Select/Hide Columns by Annotation

-

From Jalview-2.9 columns of an alignment can be filtered using - any annotation rows added to that alignment.

- To carry out this operation, navigate to "Select" menu - → "Select/Hide Columns by Annotation..." to bring - up the Select/Hide by Annotation window. The filter options vary depending +

From Jalview 2.9 columns of an alignment can be filtered using + any annotation row added to that alignment.

+ To carry out this operation, navigate to "Select→Select/Hide Columns by Annotation..." to bring + up the 'Select/Hide by Annotation' window. The filter options vary depending on the type of annotation selected. If an annotation that has a numeric values is selected, the threshold filter option is activated as seen in the figure on the right below, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.
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diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html index 990a1c9..ce7d96e 100644 --- a/help/html/features/pdbsequencefetcher.html +++ b/help/html/features/pdbsequencefetcher.html @@ -25,18 +25,16 @@ PDB Sequence Fetcher -

From Jalview 2.9 a specialised interface was introduced for +

From Jalview 2.9, a specialised interface was introduced for fast and efficient discovery/retrieval of sequence data from the PDB database. The introduced interface enables live querying of PDB data on-the-fly thereby eliminating the need to memorise database accession or to manually cross-reference other bioinformatics websites before retrieving - sequence data in Jalview. The underlying technology is provided by + sequence data in Jalview. The underlying infrastructure is provided by EBI and is based on Apache Solr which is a text based search engine.

- The PDB Sequence Fetcher interface can be opened by selecting PDB - as the choice database from the 'Select Database - Retrieval Source' interface of Sequence - Fetcher. + The PDB Sequence Fetcher interface can be accessed from "File →Fetch Sequence(s) →Select Database →PDB" click the ok button after selecting PDB from the 'Select Database + Retrieval Source' interface.

Use the drop-down menu to select a specific field to search by in the PDB database, the default - option is 'ALL'.

+ option is 'ALL'.

Furthermore, the PDB search interface also provides the following functionalities:

Customising displayed meta-data
To change - the displayed meta-data in the search result, click the 'Configure - Displayed Columns' tab, then tick off the options wanted. + the displayed meta-data in the search result, click the 'Configure + Displayed Columns' tab, then tick off the options wanted.

Importing Sequence
After querying the PDB diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index 039fdb0..1bf9f32 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -55,22 +55,22 @@ Associating PDB files with Sequences
- Discovery/Association of PDB entries to a sequence happens + 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, + 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. + 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.

+ 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.

+