[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.
Cheers,
Pavel.
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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