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Re: [modeller_usage] I have problem my protien has some area seems to be extra



Zartasha Mustansar wrote:
My template is single ...
The generated output models (i created 10 moedls with modeller) the model with best energy has some area leaning out of the structure which seems to be not included in the protien ....(When Viewed with Swiss pdb Viewer)

It looks like you have about 17 residues at your N terminus which are not aligned with the template. Since you have no homology information for these residues, Modeller has no choice but to treat them as a loop, and since the N terminus itself is not fixed, the lowest energy conformation found is most likely to be an extended chain. You will need to add some additional restraints to your system, either by introducing a template which covers the N terminus, or by manually adding extra restraints (http://salilab.org/modeller/manual/node32.html)

	Ben Webb, Modeller Caretaker
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