[phenixbb] source of fobs for refinement after AutoSol
whittle at MIT.EDU
Thu Jul 9 08:31:04 PDT 2009
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!
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?
>> 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
>>> If you supply
>>> 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
>>>> 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?
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>> 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
> 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://
> 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/
> phenixbb mailing list
> phenixbb at phenix-online.org
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