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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.</p>
- <p><strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
+ <p>
+ <strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
Configuration options controlling whether SIFTS mappings are used
can be found in the <strong>Tools → Preferences →
Structure tab</strong>, under 'Sequence ↔ Structure method'.<br /> <em>Note:</em>
<strong>Multi-Chain Mappings</strong> <br />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.
</p>
<p>To see this in action, Retrieve the UniProt sequence
FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over
<Strong>Viewing Mapping Output</Strong> <br /> The mapping provided
by the SIFTS record is accessible via <strong>File →
View mapping</strong> menu of the structure viewers. The screenshot below
- shows the mapping created between UniProt sequence FER1_MAIZE and proteins in PDB 3B2F, which reports that two 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).
<p>
 <img src="sifts_mapping_output.png" align="left"
- alt="SIFTS mapping output" />
- <br/>
+ alt="SIFTS mapping output" /> <br />
<p>
<em>SIFTS Mapping integration was added in Jalview 2.10</em>
</p>
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