[phenixbb] source of fobs for refinement after AutoSol

[Tom Terwilliger]

Hi James,

Yes, that is correct.

However if you want...you can just go on to AutoBuild and build a new  
model from scratch and generate a set of free R flags there, supplying  
your data as data=mydata.sca. I would recommend this anyway because  
AutoBuild makes a much better model than AutoSol, and including the  
model from AutoSol doesn't necessarily help (and can make it worse if  
the AutoSol model is really incomplete, such as from secondary- 
structure-only model-building). I use the AutoSol model-building just  
to see if things are going well and then I throw that model away.   
This is also the default when you use "after_autosol=True" in  
AutoBuild and when you run the AutoBuild GUI after running AutoSol. It  
is convenient to use the data and freeR in in  
exptl_fobs_phases_freeR_flags_*.mtz from AutoSol but you don't have to.

The key of course is:  once you refine a model and want to use that  
model further...you must use the set of free R flags used in that  
original refinement from then on.  If you throw away that model and  
start from scratch you can also make a new set of free R flags. The  
hexdigest REMARK in your PDB file from phenix.refine helps you make  
sure that this is done correctly.

All the best,
Tom T

On Jul 9, 2009, at 8:35 AM, James Whittle wrote:

> Dear Tom:
>
> Ok. Thanks for the quick response!
>
> I should run then run AutoSol again to get this file, and it will  
> have the HL coefficients in it?
>
> --James
>
>
> On Jul 9, 2009, at 10:13 AM, Tom Terwilliger wrote:
>
>> Hi James,
>>
>> As you are expecting, in AutoSol the file  
>> exptl_fobs_phases_freeR_flags_*.mtz normally contains the  
>> experimental Fobs and free R flags for refinement, along with  
>> phases and HL coefficients from the experimental phasing.
>>
>> However if an anisotropy correction is applied to the data, then by  
>> default no refinement is done in AutoSol and no  
>> exptl_fobs_phases_freeR_flags_*.mtz file is created.  This is to  
>> ensure that refinement is not carried out against anisotropy- 
>> corrected data (you want to refine against the original data, and  
>> have phenix.refine apply an anisotropy correction as part of  
>> refinement).
>>
>> If you supply
>>
>> input_refinement_file=my_data.sca
>>
>> then my_data.sca will be used for refinement and an  
>> exptl_fobs_phases_freeR_flags_*.mtz will be created.  Note that  
>> my_data.sca can be identical to your input data file if you want.   
>> I am guessing that in your case an anisotropy correction was  
>> applied to the data in this way.
>>
>> I hope that helps!
>> -Tom T
>> ps. I am thinking of changing the default to make  
>> input_refinement_file automatically defined if an anisotropy  
>> correction is applied so that you don't have to do this...
>>
>> On Jul 9, 2009, at 7:55 AM, whittle wrote:
>>
>>> Dear all,
>>>
>>> I have a question regarding the output of AutoSol.
>>>
>>> I've run AutoSol, using the data directly from scalepack as a .sca  
>>> file,
>>> and would like to now begin refining the structure I've built.
>>>
>>> There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the
>>> AutoSol directory. Isn't this the right file to use? Since it's not
>>> there, is it proper to use the phaser_2.mtz file for phenix.refine?
>>>
>>> --James
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>> Thomas C. Terwilliger
>> Mail Stop M888
>> Los Alamos National Laboratory
>> Los Alamos, NM 87545
>>
>> Tel:  505-667-0072                 email: terwilliger at LANL.gov
>> Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
>> PHENIX web site: http:www.phenix-online.org
>> ISFI Integrated Center for Structure and Function Innovation web  
>> site: http://techcenter.mbi.ucla.edu
>> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
>> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>


Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




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