On Wed, 2010-11-24 at 09:54 -0800, Huiying Li wrote: > >> I have two structures of the same protein superposed with the LSQ > >> Superpose in Coot by matching the first ~100 residues of the > N-terminal > >> domain. Now I'd like to calculate the pair-wise RMSD for the entire > >> pre-superposed structures (~400 residues). Can LSQKAB output RMSTAB > for > >> the two input PDB files without doing its own FIT/MATCH > calculation? >
If you save your superposed model in a separate pdb file you can use this http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Print_the_shifts_in_individual_atom_positions to get the list of individual atomic shifts. You probably don't care about all the atoms, so you can just add "| grep CA | sort -k3 -n" to the end of the command to get the list of shifts for CA's. So the full command will look like this grep 'ATOM\|HETATM' file1.pdb file2.pdb | \ grep -v REMARK | \ cut -d: -f 2 | \ cut -c 13-54 | \ sort | \ awk 'BEGIN {FIELDWIDTHS = "14 28"; pt=""} {if(pt==$1) print pr,$2; pt= $1; pr=$0;}' | \ awk 'BEGIN {FIELDWIDTHS = "14 4 8 8 8 5 8 8 8"} {printf "%s %8.4f\n", $1,sqrt(($3-$7)^2+($4-$8)^2+($5-$9)^2);}' | \ awk 'BEGIN {FIELDWIDTHS = "4 1 3 1 1 5 9"} {printf "%s %s %s %s %s\n", $3,$5,$6,$1,$7;}' | \ grep CA | sort -k3 -n Cheers, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
