[phenixbb] source of fobs for refinement after AutoSol

James Whittle whittle at MIT.EDU
Thu Jul 9 09:23:58 PDT 2009


Ok. Thank you for pointing me to that.

--James


On Jul 9, 2009, at 11:33 AM, Tom Terwilliger wrote:

> 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
>>
>> _______________________________________________
>> 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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