User guide

Note: The labels in the text string must correspond to explicit nicknames.
Expanding sequences
After creating a sequence, you can expand the whole sequence or just specific labels.
1. Select one or more labels in the sequence using lasso tool or marque tool. (Hold down the SHIFT key to select
more than one.)
2. Go to Structure>Expand Label.
When you expand a residue into its structure, the label appears below the structure.
Contracting labels
To collapse the structure back to its label (in the sequence):
1. Double-click the label to select the structure.
2. Go to Structure>Contract Label.
If you edit the label prior to contracting the structure, the new label text will be incorporated into the contracted struc-
ture. For example,consider that you modify a residue, and then change its name from Ala to Ala'. On contraction, the
sequence would contain the string Ala'.
Clean Up Biopolymer
After you contract the labels, you can use the Clean Up Biopolymer command to clean the sequence. This command
re-arranges the sequence so that the residues are aligned, and wrapped. To specify the number of 'residues per line'
and the number of 'residues per block' in a biopolymer, select the biopolymer and then go to Object > Object Settings
> Biopolymer Display tab.
Modifying sequence residues
Note: When you modify a residue structure in your drawing, to ensure that the contracted label includes your
changes, you must define a new nickname.
To modify a sequence residue.
1. If the residue in the sequence is contracted, right-click the residue and select Expand Label.
2. Modify the residue as desired.
3. Using the Text tool, rename the residue label to reflect a new structure. In the example below, the "Ser" label has
been renamed as "hSer" (for homoserine).
ChemBioDraw 13.0
Chapter 5: Drawing biopolymers 65 of 401