Limiting Zones Read From an Alignment

When obtaining fit zones from a sequence alignment, either from ALIGN or from READALIGNMENT, it can be useful to limit the zones of residues used. Normally all aligned residue pairs will be used.

For example, if the alignment were:

                       1         2         3
              123456789012345678901234567890123
              ASAHSTGEHNM--PLELLGHISLAM---NPRTY
              ---HSTADHNLRTPLEVLG--SLAMEDRQPRTY

the zones would normally be taken from the following positions in the alignment: 4-11, 14-19, 22-25, 29-33

By using the command:

      LIMIT 20 28

only the zone from 22-25 would be included.

This is particularly useful in conjunction with the ITERATE command (Section 7.4) and when fitting multiple structures (Section 8).

The LIMIT OFF command restores the default behaviour of deriving the zones from the whole alignment.