[phenixbb] source of fobs for refinement after AutoSol
terwilliger at lanl.gov
Thu Jul 9 07:13:39 PDT 2009
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!
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
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