[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] How NOT to add missing residues

On 2/8/13 12:29 AM, Anirban wrote:

I am trying to model a protein for which there is a gap (resi 65 - resi
75; a loop)between two helices. I do not wish to add the missing 10
residues and want to leave the helices unjoined . But MODELLER always
automatically joins the two helices (resi 64 with resi 76). How can I
tell MODELLER not to join the helices? Please suggest.
Add a chain break ('/' character) to your alignment between the two residues. Modeller will then treat the two parts of the sequence independently. You might want to add a weak distance restraint between the two residues though to stop them drifting too far apart. 

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