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After submitting your model query and receiving a structure, keep in mind that the accuracy of the hypothetical model may vary dramatically for given domains. Often times, in addition to accuracy scores, it is beneficial to see a per-residue accuracy which can usually be done through coloring the model by B-factor. Itasser automatically assigns per-residue modeling accuracy scores as the B-factor of its models. This can be visualized easily in the latest edition of PyMol by first opening your model and then selecting "A-->preset-->b factor putty".