Hello!
I am not sure if you've received any responses to this question yet. I had a similar problem with the C terminal of my protein that did not align with any of the templates. The solution I found was to use secondary structure prediction programs, and since they all pointed towrds an alpha helix for that region of my protein (based on its primary sequenmce) I then used restraints on Modeller to "force" that area into a helix.
I'd be glad to hear how it works out for you!
-Charlotte Habegger-Polomat Quebec, Canada
นายจิตระยุทธ์ จิตอ่อนน้อม wrote:
> > Dear Modeller users > I have a big problem in my sequence which has a long gap when i make a > multiple alignment so how modeller solve this problem. Is it built > this model from this gap? or we should cut this gap(but i don't want > to cut this sequence because this sequence is important for looking > the catalytic mechanism. Can any one help me please contact me?. > Thank you > Mr. Jitrayut Jitonnom CSML (Computer Simulation and Modeling Laboratory) > Chiang Mai University > Thailand. > > > > ---------------------------------------------------------------------------------- > > http://www.chaiyo.com ไชโยเมล์ - ฟรีอีเมล์รูปแบบใหม่ สดใสกว่าเดิม... > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >