Iterative Updating of the Fitting Zones
Keywords: ProFit

Next: Multiple Structure Fitting Up: Specifying Zones Previous: Limiting Zones Read From

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Iterative Updating of the Fitting Zones

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

Next: Multiple Structure Fitting Up: Specifying Zones Previous: Limiting Zones Read From