[phenixbb] phenix version 1.4-3: problem with bulk solvent scaling
Pavel Afonine
PAfonine at lbl.gov
Fri Jan 30 16:20:23 PST 2009
Hi Oliv,
I have a guess about what is wrong, but before I say it, could you
please send us the exact command you are using. IF you are specifying a
.def or .eff file in the command line, could you please send this .eff
or .def files as well.
Pavel.
On 1/30/2009 4:02 PM, Oliv Eidam wrote:
> Hi,
>
> I am currently refining a good 1.6 Angstroem data set using Phenix.
> Thereby I noticed a significant difference of R-free (>3%) depending on
> whether I used phenix version 1.3-rc6 (installed on my Mac laptop) or
> phenix version 1.4-3 (installed on my linux work station). Rfree differs
> by more than 3% (!) although I am using the same starting model, the
> same reflection file and the same refinement protocol (shown at the end
> of this email with detailed R and R-free factors for the 3 steps).
> In my opinion, my phenix 1.4-3 installation has a problem in the "bulk
> solvent modeling and scaling" steps. Indeed, I find in the log file that
> the "overall anisotropic scale matrix" shows all values set to zero.
> Analogous the "maximum likelihood estimate for coordinate error". This
> is true in all steps where an "overall anisotropic scale matrix" is
> calculated.
> Here is one example during 1.4-3 refinement:
>
> ====================== bulk solvent modeling and scaling
> ======================
>
> |--(resolution: 1.61 - 29.59 A; n_refl. =
> 99535)------------------------------|
> |
> |
> | r_work= 0.3419 r_free= 0.3358 ksol= 0.39 Bsol= 19.12 scale=
> 1.247 |
> |
> |
> | overall anisotropic scale matrix (Cartesian basis;
> B11,B22,B33,B12,B13,B23):|
> | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3=
> 0.00 |
> |
> |
> | maximum likelihood estimate for coordinate error: -0.00
> A |
> | x-ray target function (ml) for work reflections:
> 5.981207 |
> |-----------------------------------------------------------------------------|
>
> The same example during 1.3-rc6 refinement:
>
> ===================== bulk solvent correction and scaling
> =====================
>
> |-macro cycle = 1-(resolution: 1.61 - 29.59 A; n_refl. =
> 99537)---------------|
> |
> |
> | r_work= 0.3153 r_free= 0.3064 ksol= 0.40 Bsol= 43.79 scale=
> 1.087 |
> |
> |
> | overall anisotropic scale matrix (Cartesian basis;
> B11,B22,B33,B12,B13,B23):|
> | (-4.01,-5.36,-8.20,-0.00,2.74,0.00); trace/3=
> -5.86 |
> |
> |
> | maximum likelihood estimate for coordinate error: 0.33
> A |
> | x-ray target function (ml) for work reflections:
> 5.946583 |
> |-----------------------------------------------------------------------------|
>
> I am asking now: Did something go wrong during my Phenix installation? I
> already re-installed Phenix (no errors): same result. Do I have to
> change something in my input files? I should probably mention that
> "bulk_solvent_and_scale = True" in my input .def files.
>
> Any help appreciated. Many thanks,
>
> Oliv
>
>
> --------------------------------------------------------------------------------
> Refinement protocol and development of R and Rfree during each
> refinement round:
> --------------------------------------------------------------------------------
> 1)Rigid body refinement
> 2) Simulated annealing (5000K)
> 3) Ordered solvent (plus annealing @ 2000K)
>
> phenix version 1.3-rc6:
> 1) R=31.5, Rf=30.6
> 2) R=23.9, Rf=25.8
> 3) R=19.8, Rf=22.0
>
> phenix version 1.4-3:
> 1) R=31.6, Rf=30.6
> 2) R=27.8, Rf=29.8
> 3) R=23.7, Rf=25.2
>
>
>
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