[phenixbb] phenix version 1.4-3: problem with bulk solvent scaling

[Paul Adams]

Which version of OS X are you using? Is it earlier than 10.4.11?

On Jan 30, 2009, at 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
>
>
> -- 
> Oliv Eidam, Ph.D.
> Postdoctoral fellow
>
> University of California, San Francisco
> Dept. of Pharmaceutical Chemistry
> 1700 4th Street, Byers Hall North, Room 501
> San Francisco, CA 94158 - Box 2550
>
> Phone: 415-514-4253
> Fax  : 415-514-4260
> Email: eidamo at blur.compbio.ucsf.edu
>
>
>
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-- 
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

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