[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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