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

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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