X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fsiftsmapping.html;h=c12d45bb11359d568c304a7fa222c537ef09cd01;hb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;hp=9492d70a3f292dc686c285bc66af70ad77a09f3c;hpb=7311b7b4712a4713b687191fe6abd19145fc8252;p=jalview.git diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html index 9492d70..c12d45b 100644 --- a/help/html/features/siftsmapping.html +++ b/help/html/features/siftsmapping.html @@ -1,4 +1,24 @@ +
@@ -24,7 +44,8 @@ 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
+
+ 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:
@@ -37,11 +58,12 @@
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, 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.
+ 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, Retrieve the UniProt sequence
FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over
@@ -53,16 +75,16 @@
Viewing Mapping Output
The mapping provided
by the SIFTS record is accessible via File →
View mapping menu of the structure viewers. The screenshot below
- 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).
+ 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).
-
+ alt="SIFTS mapping output" />
SIFTS Mapping integration was added in Jalview 2.10
- \ No newline at end of file +