[phenixbb] Bulk solvent scaling problems

Pavel Afonine pafonine at lbl.gov
Tue Sep 25 12:21:41 PDT 2007

Hi Steve,

you are the second person in the last 2 years who faced the problem in 
bulk solvent correction and aniso scaling in phenix since it is 
introduced in 2005 (Acta Cryst. (2005). D61, 850-855 "A robust 
bulk-solvent correction and anisotropic scaling procedure" P. V. 
Afonine, R. W. Grosse-Kunstleve and P. D. Adams). Yes, I clearly see 
there is a problem. For me the only way to debug and fix it is to have 
your data and model so I can reproduce this problem on my computer and 
fix it. My question then: could you please send me the model and data? I 
guarantee that I will use it for fixing this bug only I will remove your 
data from my computer once the problem is fixed. Otherwise there is 
noting I can do. The protocol we have is very robust and sophisticated 
and so if it fails there is something really exceptional so I really 
need to look at the data to resolve it.


seglynn wrote:
> Dear all,
> I am using phenix.refine for the first time to refine a 4.5A structure solved by
> MR with individual sites (stretching things a bit, I know) and a grouped ADP per
> domain. Below are the R-factor per cycle stats:
> REMARK ------------------------------------------------------------------------
> REMARK  R-factors, x-ray target values and norm of gradient of x-ray target
> REMARK  stage     r-work r-free  xray_target_w  xray_target_t
> REMARK    0    :  0.6464 0.6186   7.101344e+00   7.091899e+00
> REMARK    1_bss:  0.3955 0.4006   6.825652e+00   6.806242e+00
> REMARK    1_xyz:  0.3200 0.3622   6.675328e+00   6.720706e+00
> REMARK    1_adp:  0.3201 0.3622   6.674498e+00   6.719426e+00
> REMARK    2_bss:  0.3539 0.3804   6.736883e+00   6.752128e+00
> REMARK    2_xyz:  0.3067 0.3427   6.639056e+00   6.687071e+00
> REMARK    2_adp:  0.3062 0.3423   6.638917e+00   6.687168e+00
> REMARK    3_bss:  0.3357 0.3685   6.706475e+00   6.735398e+00
> REMARK    3_xyz:  0.3082 0.3469   6.652536e+00   6.702364e+00
> REMARK    3_adp:  0.3076 0.3468   6.652984e+00   6.703972e+00
> REMARK    3_bss:  0.3286 0.3659   6.701854e+00   6.743421e+00
> REMARK ------------------------------------------------------------------------
> You can see that after the intial scaling, each cycle of bulk solvent scaling
> and anisotropy correction leads to an increase in R-factors of ~2%. Has
> anyone seen this behaviour before and maybe suggest a solution? Alternatively,
> is there a way I can turn off the final cycle of bulk solvent scaling before
> outputting the pdb and maps?
> Thanks in advance,
> Steve Glynn
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