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

Pavel Afonine pafonine at lbl.gov
Wed May 20 23:44:30 PDT 2015

> 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,

no need to convert .mrc into .ccp4 (isn't it the same thing?). Anyways, 
phenix.real_space_refine can use both.

> 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.

I need to see the files to be able to comment. If you share the files 
(off list and not sending directly via email but using things like 
Dropbox instead) then I will be happy to have a look.

>  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?

phenix.real_space_refine model.pdb map.mtz run=adp

should just do what you want. If it didn't - see above (I need to see 
the files).


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