[phenixbb] phenix version 1.4-3: problem with bulk solvent scaling
Pavel Afonine
PAfonine at lbl.gov
Fri Jan 30 16:58:44 PST 2009
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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>>
>
> --
> 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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