On Fri, 2010-08-20 at 18:50 +0200, Charles W. Carter, Jr wrote:
> Is there a program that will read in a pdb coordinate file and re-order the
> side chain atoms in each residue according to a standard order?
>
> I've a program that compares two files for the same structure, but requires
> that the order of the atoms be the same in both cases. I'm using a variety of
> files in which the residue atoms are ordered either main chain first or
> side-chain first. I've not found a suitable program in the CCP4 suite, though
> one might exist. MOLEMAN2 doesn't seem suitable, either.
>
> Thanks,
>
> Charlie
How about this
---
cut -c 13-27 a.pdb | awk '{printf "grep \"%s\" b.pdb\n",$0;}' | bash -sf
---
This will put all the atoms in b.pdb in the same order they are in
a.pdb. This definitely works on ATOM/HETATM lines, though effect on
other records may be unpredictable. And this will lose all the atoms
that are not common for both models, but you said you are looking at the
same structure.
HTH,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
