[phenixbb] Phenix.real_space_refine and B-factor

Pavel Afonine pafonine at lbl.gov
Thu Apr 30 06:36:13 PDT 2015


it does not include ADP refinement by default. You can refine B by 
adding "adp" to "run" keyword, as explained in documentation:



On 4/30/15 5:09 AM, Smith Liu wrote:
> Dear All,
> By Phenix.real_space_refine if is very nic to fit a PDB into an EM 
> map, and we can get a fitted PDB. However no matter what is the run 
> strategy (default, morphing, local grid search, etc), in the got PDB 
> the B-factors for each atom in the coordinates were always those from 
> the original input PDB, which may make the B-factors in refined PDB 
> meaningless. As finally we need to deposit the refined PDB and EM to 
> the database, will you please explain how to settle the B-factor 
> issues in the refined PDB related to Phenix.real_space_refine?
> Smith

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