Michael, I think something crudely resembling what you are asking can be done with Chimera.
Load your two PDBs and run matchmaker
Tools > Structure Comparison > MatchMaker
In the dialog box that appears, under matching, there is a box that is ticked by default "iterate by pruning long atom pairs until no pair exceeds: "
You can play with the value and see when the residues you are interested in are no longer involved in the superposition.
To see the RMSD between the atoms pairs used you need to look in the reply log (Favorites > Reply log)
Stephen
On 29 December 2010 14:52, Michael Swan
<[log in to unmask]> wrote:
Dear all,
I am having a bit of trouble finding a program to do an rmsd calculation and give me the differences between all the atoms in the structures.
I have two structures which are identical in the sense that one is the apo protein and one is the bound structure. I would like to superimpose them using only one domain then output the rmsd values for all the atoms or at least individual residues. The structures are not completely identical as some extra residues were visible in the bound structure so I hope there is a program that can ignore those differences.
If anyone knows of a program that will do this calculation I would much appreciate hearing about it. There seem to be many programs that will give an average rmsd over the whole structure or just the region used for alignment but I haven't found anything that will give me distances between atoms or residues that were not used in the alignment.
Thanks,
Mike.