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Listen to what phenix is trying to tell you: the N is the COO and the COO the N; rotate.
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<div class="">On 27 Jan 2024, at 14:52, Murpholino Peligro <<a href="mailto:murpholinox@gmail.com" class="">murpholinox@gmail.com</a>> wrote:</div>
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<div class="">What is the recommended approach to tell phenix.refine to leave the residue inside its electron density? (crystal neighbors)<br class="">
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<div class="">The green model is the input to phenix.refine, the maps and the yellow model are the output of phenix.refine. As you can see, phenix.refine will move the residue outside the density (to avoid clashes I guess?) I have tried setting the occupancy
of OXT to 0.5, but it is not good. (you can see there is a water in a special position, just above the bad residue) Any more ideas?
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