The "Align to Existing Sequence" button can be used to map and link existing sequences or sequence alignments to a protein structure chain in a Molecule Project (3D view). It can also be used to reconnect a protein structure chain to a sequence or sequence alignment previously created by Show Sequence (Show sequence associated with molecule) or Align to Existing Sequence.
Select a single protein chain in the project tree (see figure 12.17). Pressing "Align to Existing Sequence" then opens a Navigation Area browser, where it is possible to select one or more Sequence, Sequence Lists, or Alignments, to link with the selected protein chain.
If the sequences or alignments already contain a sequence identical to the protein chain selected in the Molecule Project (i.e. same name and amino acid sequence), this sequence is linked to the protein structure. If no identical sequence is present, a sequence is extracted from the protein structure (as for Show Sequence - Show sequence associated with molecule), and a sequence alignment is created between this sequence and the sequences or alignments selected from the Navigation Area. The new sequence alignment is created (see Create an alignment) with the following settings:
- Gap open cost: 10.0
- Gap Extension cost: 1.0
- End gap cost: free
- Existing alignments are not redone
When the link is established, selections on the linked sequence in the sequence editor will create atom selections in the 3D view, and it is possible to transfer annotations between the linked sequence and the 3D protein chain (see Transfer annotations between sequence and structure). Notice, that the link will be broken if either the sequence or the 3D protein chain is modified.
Two tips if the link is to a sequence in an alignment:
- Read about how to change the layout of sequence alignments in View alignments
- It is only annotations present on the sequence linked to the 3D view that can be transferred to atom groups on the structure. To transfer sequence annotations from other sequences in the alignment, first copy the annotations to the sequence in the alignment that is linked to the structure (see figure 12.20 and Copy annotations to other sequences).