[phenixbb] source of fobs for refinement after AutoSol
terwilliger at lanl.gov
Thu Jul 9 08:12:26 PDT 2009
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,
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
>>> 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?
>>> 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://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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