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Re: [modeller_usage] The large gap on sequence is a big problem



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.



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