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

Oliv Eidam eidamo at blur.compbio.ucsf.edu
Fri Jan 30 16:14:09 PST 2009


I am using 10.4.11 on OS X .
However, at the moment I am more interested in getting phenix to run 
correctly on my linux box: Fedora core 9, kernel 2.6.25.11-97.fc9.i686.
Thanks, Oliv

Paul Adams wrote:
> 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
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
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>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>     
>
>   

-- 
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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