First off, when the documentation includes square brackets in the command
it indicates optional arguments. You don't include them in the command
itself. In this case, pair_fit takes alternating selections from obj1 and
obj 2. It also requires that the number of atoms in each selection be
equal. I usually use CA atoms.
>From you example it seems like you want to align two structures in chunks
of 254 residues, but in a permuted order. I would do it as follows. I'm
going to use the shorter "/obj1///1-255/CA" syntax to stand for "obj1 and
resi 1-255 and name CA").
pair_fit /obj2///256-510/CA, /obj1///1-255/CA, /obj2///1-255/CA,
/obj1///256-510/CA, /obj2///766-1020/CA, /obj1///511-765/CA,
/obj2///511-765/CA, /obj1///766-1020/CA
Note that if you have any missing residues you might get an error 'Atom
counts between selection sets don't match'. In this case you should make
sure that the obj2 selections have the same number of atoms as the obj1
selection.
-Spencer
On Fri, Oct 21, 2016 at 12:10 AM Subha K <subhal...@gmail.com> wrote:
> Hi there,
>
> Could somebody please help me with the correct syntax for pair fit?
>
> I tried this, but this doesn't work.
>
> pairfit (obj2 and resi 256-510), (onj1 and resi 1-255), [(obj2 and resi
> 1-255), (obj1 and resi 256-510), [(obj2 and resi 766-1020), (obj1 and resi
> 511-765), [(obj2 and resi 511-765), (obj1 and resi 766-1020)]]]
>
> Thanks,
> Subha
>
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