Cn3D has a complete alignment editor when manual changes to an alignment are desired, such as to fix errors, or to add new sequences.
There are a few basic rules about the sort of editing you can do: you can't change the sequences themselves, and Cn3D's alignment model is enforced - that is, only aligned blocks with no gaps are allowed. Beyond that, however, the user has complete freedom to alter the alignment with the operations listed below.
The alignment editor works the same in both the alignment window and the import window. To turn on the editor in the alignment window, use Edit:Enable Editor; the editor in the import window is always on.
Changing the alignment
The basic alignment editing operation is simply to click-drag residues left or right within an aligned block. This will shift the alignment of that row within that single block. This assumes that Mouse Mode:Horizontal Drag is selected, which is the default when the editor is on.
After any change to the alignment, there is an Edit:Undo operation available in case a mistake is made. You can undo up to 50 operations since the editor was last enabled.
There are also operations that change the size and number of aligned blocks, described below.
The block indicator row
When the editor is on, you will see an extra row at the top of the alignment, labeled (blocks), that indicates the boundaries of the aligned blocks. The symbol '<' indicates the left edge of the block, '-' the middle, and '>' the right. If a block is a single residue wide, the '^' symbol is used.
To make a block bigger or smaller, simply click and drag the edge symbol ('<' or '>'). When making the block smaller, residue letters will be made lower case and added to the adjacent unaligned region. Or when making the block bigger, you will see more residues being added to the block - hence the letters becoming capitalized, and possibly colored in an aligned block scheme. Note that because no gaps are allowed in an aligned block, there may be a limit on how big you can make a block, depending on how many unaligned residues are available in the adjacent unaligned area in each sequence in the alignment.
Block operations
There are four block-wise operations in the editor:
- Split block: select this item then click on an internal column within an aligned block; the existing block will be split into two adjacent blocks with the new block starting at that column.
- Merge blocks: select this item then click-drag the mouse across the block edges of any two or more adjacent aligned blocks. These blocks will be fused into one single block.
- Create block: select this item and click-drag across any number of columns of unaligned residues. A new block will be created from these residues, assuming every sequence in the alignment has aligned residues in the selected columns.
- Delete block: select this item and click anywhere in an aligned block. The block will be removed and its residues added to adjacent unaligned regions.
Row operations
The editor also lets you delete a row with Edit:Delete Row, move rows up or down when Mouse Mode:Move Row is enabled, and also sort rows by various criteria - see the built-in help on the Edit:Sort Rows algorithms.