[phenixbb] source of fobs for refinement after AutoSol

Tom Terwilliger terwilliger at lanl.gov
Thu Jul 9 07:13:39 PDT 2009

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


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

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