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 mailto:[email protected]> wrote: LET OP: Deze e-mail is afkomstig van buiten de organisatie. Open alleen links of bijlagen als je de afzender kent en weet dat de inhoud veilig is. CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. 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? _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]