Hi Andrea,
It might be the B-factor problem.
The "red" densities are negative values that may be caused by neighbour atoms which were over-fitted. How was the Wilson B-factor value (and resolution) and the B-factor in the model, particularly, around the "red" region. You may need to reset the B-factor to a lower value (or apply a negative B-factor to the processed data), and refine the model again, to see if the "red" densities could disappear.
Jiansheng.
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Jiansheng Jiang, Ph.D.
Molecular Biology Section
Laboratory of Immune System Biology, NIAID/NIH
Building 10, Room 11D07
10 Center Drive
Bethesda, MD 20892-1892
U.S.A.
Phone: 301-761-6760
E-mail: [email protected]
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