just do this one-liner (assuming that your numbering is not messed up and you have "the first atom") grep 'ATOM 1' model1.pdb model2.pdb | cut -d: -f 2 | cut -c 31-54 | awk '{printf "%s ",$0;}' | awk '{print sqrt(($1-$4)^2+($2-$5)^2 +($3-$6)^2);}' On Tue, 2012-06-19 at 15:04 +0000, Claudia Millán Nebot wrote: > Hello everyone :) > > > I would like to know if it exist some tool that allows to calculate > RMSD between 2 pdbs that are identic, but just displaced in space. It > should not make a superposition, beause if this is the case it will > just say that RMSD is 0 . > I know is not such a difficult problem in terms of scripting, but i > was wondering if there are tools already. > > > Claudia Millán ([log in to unmask]) > > Institut de Biologia Molecular de Barcelona (IBMB-CSIC) > > Barcelona, Spain > > > -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs