[phenixbb] leave residue inside its electron density when neighbor is too close

[a.perrakis at nki.nl]

Listen to what phenix is trying to tell you:  the N is the COO and the COO the N; rotate.

A.

On 27 Jan 2024, at 14:52, Murpholino Peligro <murpholinox at gmail.com<mailto:murpholinox at gmail.com>> wrote:

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What is the recommended approach to tell phenix.refine to leave the residue inside its electron density? (crystal neighbors)
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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