User guide

You can also overwrite and replace the sequence atoms using the residue replacement button in the biopolymer

editor. For more information, see "Replacing residues" on page 68.

Toggle amino acids

Toggle Amino Acid Style AA1<->AA3 option lets you change the amino acid representation from single letter to tri-

ple letter and vice versa. For example,

1. Select the sequence.

2. Right-click and select Toggle from Amino Acid Style AA1<->AA3

You can also change the amino acid representation of expanded, substituted, and protected amino acids. For exam-

ple,

Toggle Amino Acid Stereo L<->D option lets you change the stereochemistry of amino acid from L to D and vice

versa.

To toggle amino acids:

1. Select the sequence.

2. Right-click and select Toggle Amino Acid Stereo L<->D.

Protecting groups

You can add protecting groups such as Trt and Fmoc to amino acids containing additional NH

or OH groups (Arg,

Aad). Protected groups are specified within brackets’()’.

To add a protecting group:

1. In a sequence, enter ‘(‘ after a completed residue name as shown below:

2. Enter the name of the protecting group and enter ‘)’ at the end of the name.

The name of the protecting group determines if it will protect the NH

or OH group. If prefixed by O, then it protects the

OH group.

You can expand and contract protected residues just like any other residue.

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