On 4/22/18 7:44 AM, Ayesha Fatima wrote:> is this the .ali file to give
for alignment.
Yes, an alignment file like that should work fine.
Which script should I use.
Since it's a chimera most conventional alignment scripts are not going
to do the right thing for you, since they will try to make a global
alignment of the two proteins, which is precisely not what you want. I
would combine them manually, unless you have another structure of a
linker region to which both will align.