From d0771875f23ab994c4f85fb6cd604378768df10e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 5 Sep 2016 17:12:50 +0100 Subject: [PATCH] JAL-2089 update Uniprot to UniProt in help docs. --- help/html/features/chimera.html | 2 +- help/html/features/dasfeatures.html | 8 ++++---- help/html/features/jmol.html | 2 +- help/html/features/pdbviewer.html | 2 +- help/html/features/seqfeatures.html | 4 ++-- help/html/features/seqfetch.html | 2 +- help/html/features/seqmappings.html | 2 +- help/html/features/structurechooser.html | 2 +- help/html/menus/alignmentMenu.html | 2 +- help/html/menus/alwfile.html | 2 +- help/html/menus/desktopMenu.html | 2 +- help/html/releases.html | 18 ++++++++++++------ help/html/webServices/dbreffetcher.html | 4 ++-- help/html/whatsNew.html | 2 +- 14 files changed, 30 insertions(+), 24 deletions(-) diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index 39dff75..0569513 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -181,7 +181,7 @@ Colours each residue in the structure with the colour of its corresponding residue in the associated sequence as rendered in the associated alignment views, including any - Uniprot sequence features or region colourings.
Pick + UniProt sequence features or region colourings.
Pick which of the associated alignment views are used to colour the structures using the View→Colour by .. sub menu. diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index 90958ae..32408ee 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -50,11 +50,11 @@

- If your DAS source selection contains sources which use Uniprot - accession ids, you will be asked whether Jalview should find Uniprot + If your DAS source selection contains sources which use UniProt + accession ids, you will be asked whether Jalview should find UniProt Accession ids for the given sequence names. It is important to - realise that many DAS sources only use Uniprot accession ids, rather - than Swissprot/Uniprot sequence names.
The The database reference fetcher documentation describes how Jalview discovers what database references are appropriate for the sequences diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index 3fa1563..3141aae 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -195,7 +195,7 @@ Colours each residue in the structure with the colour of its corresponding residue in the associated sequence as rendered in the associated alignment views, including any - Uniprot sequence features or region colourings.
Pick + UniProt sequence features or region colourings.
Pick which of the associated alignment views are used to colour the structures using the View→Colour by .. sub menu. diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index fd13f57..eca218a 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -123,7 +123,7 @@ Colours each residue in the structure with the colour of its corresponding residue in the associated sequence as rendered in the associated alignment view, including any - Uniprot sequence features or region colourings.
+ UniProt sequence features or region colourings.
Residues which only exist in the PDB structure are coloured white if they are insertions (relative to the associated sequence in the alignment) and grey if they are N or C diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 0ec5f3b..cf79858 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -29,7 +29,7 @@

Jalview can colour parts of a sequence based on the presence of sequence features - which may be retrieved from database records - (such as Uniprot), the result of sequence + (such as UniProt), the result of sequence motif searches or simply read from a sequence features file. You can also create features from the results of searches or the current selection, @@ -54,7 +54,7 @@

Since Jalview 2.08, sequence features assigned to a sequence can be organised into groups, which may indicate that the features were all - retrieved from the same database (such as Uniprot features), or + retrieved from the same database (such as UniProt features), or generated by the same analysis process (as might be specified in a sequence features file). diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 4aa7234..ff5c1b0 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -87,7 +87,7 @@

If you use the WSDBFetch sequence fetcher services (EMBL, - Uniprot, PFAM, and RFAM) in work for publication, please cite:

+ UniProt, PFAM, and RFAM) in work for publication, please cite:

Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html index 60ac6ab..d868cc5 100644 --- a/help/html/features/seqmappings.html +++ b/help/html/features/seqmappings.html @@ -40,7 +40,7 @@ correspondence between DNA and protein sequences. This mapping can be imported directly from EMBL and EMBLCDS database records retrieved by the Sequence Fetcher, and - allows sequence features to be mapped directly from Uniprot das + allows sequence features to be mapped directly from UniProt das sources to their coding region on EMBL sequence records.

In Jalview 2.9.1 SIFTS Mapping was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence

diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index 296a751..f5f5916 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -75,7 +75,7 @@ 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, + 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. diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index ce339cc..5739797 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -33,7 +33,7 @@