[phenixbb] reflection file utility and use of modified phases in refinement

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Aug 28 07:47:22 PDT 2009


Hi Engin,

Thanks, yes, I see now what you are looking at:

 ---  Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM
FreeR_flag ---
 hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz

The file exptl_fobs_phases_freeR_flags.mtz has a copy of the
(experimental) HL coefficients that were input to autobuild.  The labels
HLAM HLBM etc are indeed confusing...they have the ending "M" because they
were copied by resolve and it outputs HLAM etc...but in fact they are not
density modified, just copied straight from the input data file.

Thank you for pointing that out.
All the best,
Tom T


>> Hi Tom,
>>
>> My second question was about autobuild recommending modified phases to
>> be used in further refinement.
>> This is the end of the log file printed by autobuild. See the line for
>> "Data for refinement":
>>
>> Summary of output files for Solution 3 from rebuild cycle 4
>>
>> ---  Model (PDB file)  ---
>> pdb_file: AutoBuild_run_1_/cycle_best_4.pdb
>>
>> ---  Refinement log file ---
>> log_refine: AutoBuild_run_1_/cycle_best_4.log_refine
>>
>> ---  Model-building log file ---
>> log: AutoBuild_run_1_/cycle_best_4.log
>>
>> ---  Model-map correlation log file ---
>> log_eval: AutoBuild_run_1_/cycle_best_4.log_eval
>>
>> ---  2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT
>> FOFCWT PH
>> FOFCWT ---
>> refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_4.mtz
>>
>> ---  Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM
>> FreeR_flag ---
>> hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz
>>
>> ---  Density-modification log file ---
>> log_denmod: AutoBuild_run_1_/cycle_best_4.log_denmod
>>
>> ---  Density-modified map coefficients FP PHIM FOM ---
>> hklout_denmod: AutoBuild_run_1_/cycle_best_4.mtz
>>
>> If HLAM, HLBM, HLCM and HLDM are density-modified phases, it looks like
>> that's what autobuild suggests.
>>
>> Thanks again,
>>
>> Engin
>>
>> On 8/28/09 7:07 AM, Thomas C. Terwilliger wrote:
>>> Hi Engin,
>>>
>>> I'm not sure about your main question...I hope that Nat or Pavel will
>>> answer you on that.
>>>
>>> On the use of density-modified phases in refinement: AutoBuild expects
>>> experimental phases in the data file, with experimental HL coefficients,
>>> and it by default it will use those HL coefficients in refinement with
>>> an
>>> MLHL target.
>>>
>>> The phase probabilities from resolve statistical density modification
>>> are
>>> pretty accurate, and not inflated, so you could use them in refinement
>>> if
>>> you wanted to. I don't suggest it, however, because the
>>> density-modification phase information is not fully independent of the
>>> other information used in refinement (e.g., a flat solvent is implicit
>>> in
>>> your refinement already, so including that through density modification
>>> is
>>> partially redundant).
>>>
>>> ps: I hope AutoBuild doesn't recommend using density-modified phases in
>>> refinement, so if you could send me the text where it says that, I will
>>> check that out!
>>>
>>> All the best,
>>> Tom T
>>>
>>>
>>>>> Hi everybody,
>>>>>
>>>>> I had some trouble with the reflection file utility today. I've been
>>>>> trying to import Rfree-flag column from one of the mtz's to my
>>>>> combined
>>>>> mtz, and it never does. The R-free flag is always left out of the
>>>>> output
>>>>> even when I have it selected. Have you guys seen this (I'm using 147)?
>>>>>
>>>>> Another question I have is about the output of phenix.autobuild.
>>>>> Phenix.autobuild tells me to use modified phase probabilities (HLAM,
>>>>> etc.) in refinement. I am assuming this is density-modified phases.
>>>>> But
>>>>> I've always thought that this would be bad practice (possibly because
>>>>> of
>>>>> unrealistically high FOMs and possible flattening of loops, etc, but
>>>>> maybe resolve does a better job than, say DM). Any ideas on that one?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Engin
>>>>>
>>>>> --
>>>>> Engin Özkan
>>>>> Post-doctoral Scholar
>>>>> Dept of Molecular and Cellular Physiology
>>>>> Howard Hughes Medical Institute
>>>>> Stanford University School of Medicine
>>>>> ph: (650)-498-7111
>>>>>
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org
>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>>
>>>>>
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>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
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>>>
>>
>>
>> --
>> Engin Özkan
>> Post-doctoral Scholar
>> Laboratory of K. Christopher Garcia
>> Howard Hughes Medical Institute
>> Dept of Molecular and Cellular Physiology
>> 279 Campus Drive, Beckman Center B173
>> Stanford School of Medicine
>> Stanford, CA 94305
>> ph: (650)-498-7111
>>
>>




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