Before analyzing a protein using Pronto, the amino acid sequence of the protein must be known. Pronto can handle proteins divided into several chains.
The amino acid sequence is entered into the Sequence Window. An example of that is shown in Figure 1. The browser at the top lists the different chains in the sequence (in this case there is only one chain). Pressing New creates a new, empty chain. Currently, the chains are named using the letters A, B, C, etc. The First Pos field is used to indicate, if the residue numbers of the particular chain does not start with number one. In the example shown, the protein is normally expressed without the first 20 amino acids known from the wildtype.
When you start with an empty database, create the chain(s) in the protein using the New button, select the chains one by one, and fill in the sequence using the lower browser. A new residue is appended to the C-terminal by focusing on the last residue (if not already so), and pressing the After button. If the chain is empty, pressing either Before or After will insert the first residue. The name of the residue is selected using the Set AA button. This button will pop up a list of the amino acids known to the program.