Hi Smith, "local_grid_search" should do it if there is reasonable density. I'm still optimizing it for cases of no density. https://www.phenix-online.org/presentations/real_space_refine.pdf Pavel On 4/28/15 8:51 PM, Smith Liu wrote:

Dear All, If with phenix.real_space_refine, I got a model (with PDB), in which there is a fragment containing several residues (not in continuation in the fragment), with side chains not fitting to the corresponding side chain density (or out of the density, but close to the density), which function(s) of phenix.real_space_refine (for example,minimization_global or local_grid_search?) can improve the fitting of the sidechains to the density? I am looking forward to getting your reply. Smith

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