Keywords: ProFit

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## Reading an Alignment

If you have an alignment performed outside ProFit you may use this to specify the equivalent zones. Any previously defined fitting zones are automatically cleared first. As with the `ALIGN` command, this can currently only be used with structures having a single chain.

The alignment should be a file in PIR format using - characters to align the sequences. The two sequences are represented by separate entries, i.e. each must have a header of the form:

    >P1;xxxxxx
    title text .......

If the PIR file contains multiple chains, it will be rejected. The first sequence will be assumed to be that of the the reference structure and the second is that of the the mobile structure. Any other sequences in the file are ignored.

The `READALIGNMENT` command is used to read in the PIR file.