Transfer annotations between sequence and structure

The Transfer Annotations dialog makes it possible to create new atom groups (annotations on structure) based on protein sequence annotations and vice versa.

You can read more about sequence annotations in Working with annotations and more about atom groups in Create atom group.

Before it is possible to transfer annotations, a link between a protein sequence editor and a Molecule Project (a 3D view) must be established. This is done either by opening a sequence associated with a protein chain in the 3D view using the 'Show Sequence' button (see Show sequence associated with molecule) or by mapping to an existing sequence or sequence alignment using the 'Align to Existing Sequence' button (see Link sequence or sequence alignment to structure).

Invoke the Transfer Annotations dialog by selecting a linked protein chain in the Project Tree and press 'Transfer Annotations' (see figure 9.12).

Image TransferAnnotationsSequenceStructure_button_markup
Figure 9.12: Select a single protein chain in the Project Tree and invoke "Transfer Annotations".

The dialog contains two tables (see figure 9.13). The left table shows all atom groups in the Molecule Project, with at least one atom on the selected protein chain. The right table shows all annotations present on the linked sequence. While the Transfer Annotations dialog is open, it is not possible to make changes to neither the sequence nor the Molecule Project, however, changes to the visualization styles are allowed.

Image TransferAnnotationsSequenceStructure
Figure 9.13: The Transfer Annotations dialog allow you to select annotations listed in the two tables, and copy them from structure to sequence or vice versa.

How to undo annotation transfers

In order to undo operations made using the Transfer Annotations dialog, the dialog must first be closed. To undo atom groups added to the structure, activate the 3D view by clicking in it and press Undo in the Toolbar. To undo annotations added to the sequence, activate the sequence view by clicking in it and press Undo in the Toolbar.

Transfer sequence annotations from aligned sequences

It is only annotations present on the sequence linked to the 3D view that can be transferred to atom groups on the structure. If you wish to transfer annotations that are found on other sequences in a linked sequence alignment, you need first to copy the sequence annotations to the actual sequence linked to the 3D view (the sequence with the same name as the protein structure). This is done by invoking the context menu on the sequence annotation you wish to copy (see figure 9.14 ).

Image SequenceAlignmentCopyAnnotations
Figure 9.14: Copy annotations from sequences in the alignment to the sequence linked to the 3D view.