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

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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] 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