Keywords: ProFit

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## Sequence Alignment

Another way of specifying zones is to let the program do it. ProFit does not provide any facilities for calculating structural equivalences, but does allow you to perform a simple Needleman and Wunsch sequence alignment and to apply zones automatically derived from that sequence alignment. This is done by issuing the `ALIGN` command. The sequence alignment is displayed, any currently active fitting zones are cleared and replaced by zones derived from the alignment.

Currently the `ALIGN` command may only be used if the structures contain only one chain.

Additional zones may also be specified in the usual way.

Clearly, it will normally be necessary to use the `ATOMS` command to specify that only backbone or C atoms are included in the fitting.

The `GAPPEN` command allows you to specify an integer gap penalty for the sequence alignment performed by the `ALIGN` command. The default value is 5.