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The third step is to improve the structural quality of the final ensemble members
(like Ramachandran plot or 3D packing interactions
) by using YASARA's most accurate simulation techniques: explicit solvent
, electrostatics without cutoff and force fields optimized for protein structure refinement
. This is done by the macro 'nmr_refinewater' in several cycles. The structure with the lowest
restraint violation energy then becomes the final ensemble member.
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