[modeller_usage] constrain template secondary structure in energy minimization/loop building

[Frank Peelman <>]

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I'm modellling an Immunoglobulin-type domain.
When generating the homology models using automodel, the beta sheet structure in
the models seems to be disturbed when compared to the template.  This is
obviously an error in the model as the besta-sheets are conserved in every
related family member. As expected, the problem occurs in the loop building and
energy minimization steps, as i do not see the loss of beta-sheet structure when
using "a.make("exit=2")".
What is the best way to avoid loss of beta-sheet structure, e.g. by tethering,
restraining sec. structure ...?