[phenixbb] R factor with no bulk solvent and anisotropic scale

[Pavel Afonine]

Hi Shunsuke,

at first glance, I don't see anything to worry about. It was a mistake 
to print this information at all:

R-work = ..., R-free = ... (no bulk solvent and anisotropic scale)

and I will probably remove it in one of the next versions.

Your start values really are:

Start R-work = 0.2665, R-free = 0.3195

and the final ones:

Final R-work = 0.2578, R-free = 0.3126.

Thanking some more...
Actually, I don't understand why this is the case:

Start R-work = 0.3762, R-free = 0.4043 (no bulk solvent and anisotropic 
scale)
Final R-work = 0.5019, R-free = 0.5204 (no bulk solvent and anisotropic 
scale)

- it is weird. If you send me (to my email address, not to the whole bb) 
the data and model then I will be able to provide some more diagnostics.

Are you using a recent version of PHENIX ? Is it not a result of running 
TLS refinement first and then running a refinement without TLS - that 
would explain this, actually, since the ANISOU all will be converted to 
isotropic equivalents.

Pavel.



On 5/6/10 8:00 PM, Shunsuke Tagami wrote:
> Dear phenixbb
>
> I am refining a low resolution data (4.1 A).
> I first refined my data with CNS, then I am trying TLS refinement with 
> Phenix.
> Although R-factors with bulk solvent and anisotropic scale are 
> reducing, R-factor without them are increasing much.
>
> Start R-work = 0.3762, R-free = 0.4043 (no bulk solvent and 
> anisotropic scale)
> Final R-work = 0.5019, R-free = 0.5204 (no bulk solvent and 
> anisotropic scale)
>
> Start R-work = 0.2665, R-free = 0.3195
> Final R-work = 0.2578, R-free = 0.3126
>
> Why are R-factors with no bulk solvent and anisotropic scale 
> increasing so much?
>
> Thanks,
>
> Shunsuke
>
>
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