Keywords: ProFit

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# Calculating the RMSd Over Other Zones and Atoms

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 6 and 7.

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.