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.