Having fitted the structures using the ZONE and ATOMS
commands to specify which residues and atoms should be included in the
fitting, the RMS deviation may then be calculated over a different
region of the structure and/or a different atom set.
This is achieved using the RZONE and RATOMS
commands. The syntax of these commands is identical to that of the
ZONE and ATOMS commands described in
Sections 8 and 9.
As each RZONE or RATOMS command is given, the RMS
deviation is reported over the new set of zones or over the new atom
set. Don't forget the RZONE commands are cummulative, like the
ZONE commands. Note that the RZONE * or RZONE
CLEAR behaves slightly differently from ZONE * or
ZONE CLEAR since it resets the zones to be the same as
those specified for the fitting using ZONE, ALIGN or
READALIGNMENT commands.
The DELRZONE command specifies zones to be deleted from the list of
user-defined zones for calculating the RMSd. The DELRZONE command uses
the same syntax as the DELZONE command. The command matches the
specified zone with a zone in the user-defined list of RMSd calculation zones
and deletes the matching zone from the list. Unlike the RZONE command,
entering either DELRZONE ALL or DELRZONE * will delete all
user-defined RMSd calculation zones rather than returning to the default
condition where the RMSd calculation zones are set to the user-defined fitting
zones. Thus avoiding the somewhat counterintuitive situation where deleting
the last RMSd zone restores all RMSd zones. If no RMSd calculation zones are
defined then ProFit will calculate the RMSd over all residues.