Re: [modeller_usage] I have problem my protien has some area seems to be extra
To: Zartasha Mustansar <>
Subject: Re: [modeller_usage] I have problem my protien has some area seems to be extra
From: Modeller Caretaker <>
Date: Mon, 03 Jul 2006 11:34:19 -0700
Cc:
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)