X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fsiftsmapping.html;h=c12d45bb11359d568c304a7fa222c537ef09cd01;hb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;hp=80c0294a5e30c8c2bd808800122beb87163daf10;hpb=68cd75cd1fea4f2c184ab031286f4ef0e9fd5f2e;p=jalview.git diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html index 80c0294..c12d45b 100644 --- a/help/html/features/siftsmapping.html +++ b/help/html/features/siftsmapping.html @@ -1,4 +1,24 @@ + @@ -21,9 +41,9 @@ 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. + 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 @@ -38,33 +58,33 @@ 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 - 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. + 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 mappings for two chains. The + mapping method is also reported (highlighted with red border).

 SIFTS mapping output + alt="SIFTS mapping output" />

SIFTS Mapping integration was added in Jalview 2.10

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