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

Oliv Eidam eidamo at blur.compbio.ucsf.edu
Fri Jan 30 16:47:29 PST 2009


Hi Pavel,

Yes, I am specifiying .def files in the commands. The commands used are:
1) phenix.refine input.mtz input.pdb strategy=rigid_body
2) phenix.refine input_refine_002.def simulated_annealing=true
3) phenix.refine input_refine_003.def ordered_solvent=true

I send you the .def and .log files in a separate email.

Thanks, Oliv


Pavel Afonine wrote:
> 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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-- 
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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