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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 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.


next up previous
Next: Obtaining Output Up: ProFit Version 3.1 Previous: Multiple Structure Fitting
Andrew Martin 2010-09-28