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[modeller_usage] query!!!

Dear Ben,
Actually i want to ask about a very common concept about modelling.... for this alignment, the red color representing beta strands is aligned with gaps and its the template part wch is aligned wth gaps, my question is how would this part be modelled???  would it be modelled a strand in predicted model??? and what if any part of target is aligned wth gaps but was conserdered a helix????? how would it be modelled..
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Albeit its a childish question, but it can clear my concept and i can edit the alignment to get a good model then..
thanking in advance