From 7311b7b4712a4713b687191fe6abd19145fc8252 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 23 Sep 2016 16:02:49 +0100 Subject: [PATCH] =?utf8?q?JAL-1957=20JAL-1479=20tweak=20SIFTS=20mappings=20d?= =?utf8?q?ocumentation,=20add=20to=20what=E2=80=99s=20new=20section?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/help.jhm | 1 + help/helpTOC.xml | 2 +- help/html/features/siftsmapping.html | 24 +++++++++++------------- help/html/whatsNew.html | 5 +++-- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index 1760d43..7e14204 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -141,6 +141,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index ed95a61..bf1710c 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -25,7 +25,7 @@ - + diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html index 80c0294..9492d70 100644 --- a/help/html/features/siftsmapping.html +++ b/help/html/features/siftsmapping.html @@ -21,11 +21,10 @@ record and use that information to construct a mapping between the sequence and downloaded structure.

If, for some reason, no SIFTS mapping data exists, then Jalview - will generate a mapping using its built-in Needleman and Wunsch - global alignment algorithm. This method of mapping was used for all - structures prior to version 2.10. -

- Controlling and troubleshooting SIFTS mappings
+ will generate a mapping using the built-in Needleman and Wunsch + global alignment algorithm. This is how sequence-structure mappings + were created before version 2.10.

+

Controlling and troubleshooting SIFTS mappings
Configuration options controlling whether SIFTS mappings are used can be found in the Tools → Preferences → Structure tab, under 'Sequence ↔ Structure method'.
Note: @@ -38,30 +37,29 @@ Multi-Chain Mappings
SIFTS gives Jalview the ability to display multi-chain mappings between UniProt sequences and PDB structure data. This is important when working with - multimeric proteins, since the biological unit will contain several + multimeric proteins, when the biological assembly can contain several structures for the same protein sequence. Multi-chain mapping allows all residues in a structure to be located in the alignment, and also, when shading the structure by sequence colours, enables conservation patterns between oligomer interfaces to be explored.

-

To see this in action, load uniprot sequence for FER1_MAIZE - then veiw PDB structure for 3B2F, you will notice that mousing over +

To see this in action, Retrieve the UniProt sequence + FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over the sequence results to two positions being highlighted in the - structure, also colouring the sequence transfers the color to all + structure, and colouring the alignment transfers the color to all the mapped chains in the structure.

Viewing Mapping Output
The mapping provided by the SIFTS record is accessible via File → View mapping menu of the structure viewers. The screenshot below - is the mapping output for the {FER1_MAIZE ↔ - 3B2F} example described above, and confirms that all two chains - were mapped. The mapping method used can be seen within the area - highlighted with red boarder. + shows the mapping created between UniProt sequence FER1_MAIZE and proteins in PDB 3B2F, which reports thattwo chains + were mapped. The mapping method is also reported (highlighted with red border).

 SIFTS mapping output +

SIFTS Mapping integration was added in Jalview 2.10

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index ac48313..1d2367d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -52,8 +52,9 @@
  • More accurate structure mappings. Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) - to match structures to UniProt sequences, even for structures - containing multiple copies of a sequence.
    • + to match structures + to UniProt sequences, even for structures containing + multiple copies of a sequence.
  • Import structures as mmCIF. Jalview now downloads data from the EMBL-EBI's PDBe site as mmCIF. mmCIF files allow Jalview to handle very large structures, -- 1.7.10.2