User guide

Note: The SHIFT key acts as a toggle. Hence, to enter D-amino acids, press SHIFT while entering a single-letter
sequence while in L mode. Alternatively, to enter L-amino acids while in D mode, press SHIFT while entering a sin-
gle-letter sequence.
Note: You can enter three letter amino acids using the "Biopolymer editor" on page 61, and you can use either the
keyboard or toolbar to enter residues.
DNA tool. Create a DNA chain using labels that represent each of the nucleic acids.
RNA tool. Create an RNA chain using nucleic acid labels.
1. Click where you want to start the sequence. A text box appears.
2. In the text box, enter the single-letter label for the residue.
Note: For a list of residue labels, see "IUPAC codes" on page 70.
3. Repeat step 2 for each residue.
4. When your chain is complete, press ENTER, or Esc.
By default, when creating a sequence, new residues are inserted after the current active residue. The insertion point is
indicated by an orange chevron. You can overwrite or replace a sequence atom using the residue replacement button.
You can also replace a sequence atom by hovering over a residue and pressing a hotkey, when no active residue is
present.
Biopolymer editor
The Biopolymers toolbar contains a new tool called Biopolymer Editor.
Using the biopolymer editor, you can create a sequence by explicitly specifying the residue name instead of the
IUPAC code. When you enter a letter, the auto-completion feature will suggest a match with a known residue in the
library. For example, when you enter 'a', the residue 'Ala' is suggested. To accept the suggestion, press SPACE or
ENTER key. Press TAB to move the caret to the end of the selected label.
To enter b amino acids, type a nickname such as bAla. The ‘b’ will be converted to the b symbol. You can also create
b amino acids using the b- amino acid button in the biopolymer editor. b- amino acids are always displayed using three
letter codes. Glycine does not have a beta carbon, and so there is no beta version.
To enter D-amino acids, specify "d-" before the residue name. Glycine is also achiral and so does not have a D ver-
sion.
Note: Use the D- amino acid and b- amino acid buttons simultaneously to produce D-b amino acids.
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