[phenixbb] on B-factor refine of the phenix.real_space_refine

Smith Liu smith_liu123 at 163.com
Wed May 20 23:05:35 PDT 2015

Dear All,
I have a EM map (.mrc), with fitting and based on a crystal structure I got the fitted PDB file. I convert the mrc map to the CCP4 map, and I run phenix.real_space_refine model.pdb map.mtz run=adp, with phenix-dev-2034, in order to get my own b-factors for my fitted PDB based on my EM map. However after the above phenix.real_space_refine, I checked the refined PDB, and I find phenix.real_space_refine neither change the coordinates, nor change the b-factors for each atom.
Thus will you please introduce to me how can I get my own b-factors for my fitted PDB in order to deposit my map and fitte pdb to the EM database?
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