Sir,

The rest of the target protein is in the form which I want (requires no modelling). So after modelling the residues 700-900, I want to join the modelled region back to the 1-699,901-1200. How can I do this? Could you please give any suggestion?

Sent from Mail for Windows 10

On 10/26/20 4:02 AM, Sruthi Sudhakar wrote:

> I would like to know if it is possible to model

> just this residue 700-900 with respect to my template to get it into the

> active form.

Sure, just include only the 700-900 sequence in your alignment for the

target (model) and align it with the relevant section of your template.

> If yes, should I use the whole protein template or the

> region corresponding to the one which I want to model in my target

> protein?

Whichever works best for you. You can include the whole template if you

like and just align it with gaps (-) in the target sequence in regions

where you don't want to use it in the model (i.e. residues 1-699,

901-1200). Or read only residues 700-900 from the template and align

just that with your model.

> Also after modelling this residues, How could I combine this

> back to the rest of the target protein.

If the rest of the protein is disordered, there is little point in

modeling it.

                Ben Webb, Modeller Caretaker

--

modeller-care@salilab.org             https://salilab.org/modeller/

Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage