The ITERATE command switches on the iterative updating of
fitted zones during subsequent FIT commands. The ITERATE
command ma be followed by an optional parameter to specify the cutoff
used to include or exclude pairs from the zones. (ITERATE OFF
is used to switch it off again.)
Currently the ITERATE command may only be used if the structures
contain only one chain.
Note that this immediately does an ATOMS CA since iteration of
zones is only performed on C
atoms. The program gives an
informational message to this effect. See notes below if you want to
calculate an RMSd over other atoms.
After the initial fit on the specified zones, the zones are updated
such that residue pairs with C
atoms within a specified cutoff
(default 3.0Å) are included and those more distant are excluded. The
optimum set of equivalences is obtained using a dynamic programming
method.
After updating the zones, the structures are refitted and the
procedure iterates to convergence of <0.01Å, (typically 3 or 4
cycles). The RMSd on C
atoms is shown after each cycle unless
the QUIET command is given.
You may specify a minimal initial zone of say 3 amino acids on which
to fit first. The zone iteration will expand the zones until as many
residues as possible can be equivalenced. Alternatively, this option
is particularly useful in conjunction with the ALIGN
command. Using ALIGN followed by ITERATE gives a
particularly convenient method of fitting two arbitrary structures.
As stated above, the ITERATE command implies
ATOMS CA. Having fitted on C
atoms, you can of course
display the RMSd over other atom sets in the usual way using the
RATOMS command (e.g. RATOMS N,CA,C,O will display the
backbone RMSd).
Should you wish to refit on another atom set using the iterated zones,
simply use ITERATE OFF to switch off iteration, select the atom
set required using the ATOMS command and use FIT to
refit the structures in the usual way. For example, to fit on backbone
atoms:
ITERATE OFF ATOMS N,CA,C,O FIT