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.