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If I apply a distance or a scaffold constraint, will it always be obeyed?


No, it will not always be obeyed. If a distance constraint or a scaffold constraint is applied, then a harmonic penalty term is added to the scoring function to reward poses that satisfy the constraint. The spring constant is set by the user when the constraint is set up. If a low spring constant is used, then solutions may be returned that do not satisfy the constrain very well.