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

[Charlotte Habegger-Polomat <chpoloma AT rsvs.ulaval.ca>]

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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