The alignment viewer has two display regions: on the left is the name of the sequence and on the right is displayed the sequence itself. The alignment viewer uses the color schema of Cn3D to display the sequence, i.e. both viewers share the same colors.

How to select residues?

- Selecting a single residue : click and release the left mouse button on the desired residue. Using this procedure along with the [CTRL] key allows you to select several residues.
- Selecting a range of residues : click and hold the left mouse button on the first residue. Then, drag the mouse to the last residue and release the mouse button. Using this procedure along with the [CTRL] key allows you to select several ranges.
- Multiple selection : press the [CTRL] key before you start to select any residue or range of residues.
- Extending a selection : to extend a selection, press the [SHIFT] key before you start to select new residue(s). Doing this will select the residues located between the current mouse position and the closest selected residue.
- Removing all selections : move the mouse to the top-left corner of the alignment viewer, then click and release the left mouse button.

All selections made inside the alignment viewer will also be highlighted on the corresponding 3D structure in the Cn3D window.

If a sequence is duplicated in the alignment viewer, the selection will appear on all instances of the sequence.

How to hide or show a row in an alignment?

Use the command Alignment | Show or Hide Rows. Deselecting a sequence description in the dialog will cause it to be hid in both the alignment viewer and the structure viewer.

You may not show less than two rows or hide the master sequence (if the alignment has one).

How to examine a single sequence (including features)?

Double click on the sequence name and the sequence viewer will appear.

How to get a description of the sequence?

Click and hold down the mouse on the sequence name. The description will appear in the status bar.

How to add a new row to the alignment?

Use the command Alignment|Add New Row. You can either add a sequence from a fasta file or download the sequence from Entrez. You have the option of using gapped or ungapped blast to do the alignment, which is done by a pairwise alignment against the master sequence.

How to close the viewer?

Use the command File|Quit to close the viewer.

How to modify the display layout?

Use the command Options|Styles to set ruler styles and positions. For displays with more than one alignment (known as a discontinuous alignment or an alignment with several blocks) you can change what is displayed between the aligned sections. For example, you may wish to display blank space instead of unaligned sequence.