Hi Tjaart,
There are two 'SET KNOWNS' in your top script, instead try this
SET KNOWNS '1eye' '1DY3'
I don't knwo if it'll make a difference but I always give them all in one
line and it works for me!
HTH
raghu
> Hi there
>
> I would like to model a multidomain protein but when I follow the
> instructions given in the manual I only only get a model based on the
> first structure in my alignment file. It totally ignores the second
> structure. There is no overlap between the domains.
>
> The top file and alignment file is attached.
>
> Can anyone help?
>
> Thanks!!
>