[phenixbb] source of fobs for refinement after AutoSol

Tom Terwilliger terwilliger at lanl.gov
Thu Jul 9 08:33:36 PDT 2009


Hi James,

Yes, say:

include_input_model=False

and it will do just what you said:

       include_input_model= True The keyword include_input_model defines
                            whether the input model (if any) is to be  
crossed
                            with models that are derived from it, and  
the best
                            parts of each kept. It also defines  
whether the
                            input model is to be included in  
combination steps
                            during initial model-building. Note that if
                            multiple_models=True and  
include_input_model=True
                            then no initial cycle of randomization  
will be
                            carried out and the keyword
                            multiple_models_starting_resolution is  
ignored. In
                            most cases you should use  
include_input_model=True
                            If you want to generate maximum diversity  
with
                            multiple-models then you may wish to use
                            include_input_model=False. Also if you  
want to
                            decrease the amount of bias from your  
starting
                            model you may wish to use
                            include_input_model=False.
-Tom T

On Jul 9, 2009, at 9:31 AM, James Whittle wrote:

> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> _______________________________________________
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> phenixbb at phenix-online.org
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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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