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
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