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Re: [modeller_usage] Optimization or Refinement of Homology Model

David Piper wrote:

1)  What level of refinement or MD_LEVEL is used as a
    default?


refine_1. See bin/__defs.top and bin/__refine.top.
2) After modelling, if there are "bumps" or poorly defined bond lengths or angles (based on ProCheck output), what is the preferred way of optimizing them?
You can use more rigorous refinement, or build more models and take the best ones. 

	Ben Webb, Modeller Caretaker
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