Re: [modeller_usage] modeling a chimeric protein

[Modeller Caretaker <>]

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.

	Ben Webb, Modeller Caretaker
--
             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage