[phenixbb] source of fobs for refinement after AutoSol

[James Whittle]

Ok. Good to know that I can do that. I did already try AutoBuild, and  
found that it got stuck.

I also have a partial, 100% identical, molecular replacement model of  
1/3 the structure, so I may try giving that to AutoBuild as well to  
see if it can help.

Is there perhaps a means to tell AutoBuild not to re-build the partial  
model, only to refine it and work on the rest?

Thanks for your help!
--James


On Jul 9, 2009, at 11:12 AM, Tom Terwilliger wrote:

> 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
>>>>
>>>> _______________________________________________
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>>>
>>>
>>> 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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>>> 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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