[phenixbb] phenix version 1.4-3: problem with bulk solvent scaling
Oliv Eidam
eidamo at blur.compbio.ucsf.edu
Fri Jan 30 17:13:53 PST 2009
Setting "minimization_b_cart = True" does the job.
Many thanks for the fast replies and help!
Oliv
Pavel Afonine wrote:
> Hi Oliv,
>
> I now see the problem... It is a bug in phenix.refine that we fixed
> sometime ago and the next PHENIX release will have it.
>
> If you go into your .def file and replace "minimization_b_cart =
> False" with "minimization_b_cart = True" that will fix the problem.
>
> If you see something like this in future, always make sure that
> "minimization_b_cart = True" in your input parameter file.
>
> Please let me know if this helped or if you have any other problems.
>
> Pavel.
>
>
> On 1/30/2009 4:47 PM, Oliv Eidam wrote:
>> 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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>>> phenixbb at phenix-online.org
>>> 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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--
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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