Having read in a reference and a mobile structure, you actually fit
them by giving the
FIT command. When you do this, you will get
a message like:
Fitting structures... RMS: 0.366
However, this will only work if the two structures are of identical composition i.e. if the sequences are the same and the same atoms are present in both. If there are any mismatches, the first such mismatch will be reported and the RMS deviation will not be calculated.
Since you will frequently need to fit non-identical structures, you
may use the
ATOMS commands to specify which
residues should be considered equivalent and which atoms should be
considered in the calculation.
If you are using zone or atom specifications, the RMS deviations will be displayed over the atoms and zones specified in those commands.
Normally the fitting procedure will not be completed if there are
any mismatched atoms or atoms missing from one of the two structures.
The program issues an error message about atoms missing in the mobile
structure which are found in the reference structure. The
IGNOREMISSING command causes the program to issue a warning
instead of an error and the fitting proceeds ignoring the mismatched
atoms. The default behaviour is restored by using the