[phenixbb] on phenix.real_space_refine

Pavel Afonine pafonine at lbl.gov
Tue Apr 28 21:21:47 PDT 2015

Hi Smith,

"local_grid_search" should do it if there is reasonable density. I'm 
still optimizing it for cases of no density.



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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