Hi Spencer,
Thanks a lot for that very useful information.
Regards,
Subha
On Tue, Oct 25, 2016 at 4:48 AM, Spencer Bliven <spencer.bli...@gmail.com>
wrote:
> 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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