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My question is about Modeller restraints. Have you ever used
of special_restraints or add_rsr to add your own restraints? Or to
build conserved part of your target protein (such as ligand binding site or
binding state of ligand)?Did Modeller build a model without any
violation of your restraints? My target protein has a
conserved ligand binding site.But even when I give it the restraints ,it
doesn't work exactly.(e.g. I gave it distance restraints with mean=2.3
Å and
std=0.03 Å
and one of pair_atom were in 3.7 Å from each other) Is it
common?Even about conserved parts of structure? Thanks
Maryam
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