[phenixbb] Confused by the output from Phenix autobuild jobs

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Nov 27 05:40:16 PST 2009

Hi Serah,

You are right that the coefficients that you want for a difference map are
not present in the overall_best_refine_map_coeffs.mtz file.  The
coefficients in that file (labelled FP PHIM) are the same as 2FOFCWT
PH2FOFCWT from the refinement output, but there are no difference map
coefficients.  I will change this.

In the meantime, I would do this after the end of autobuild:

phenix.refine AutoBuild_run_1_/overall_best.pdb \

and then you will have your map coefficients.

>> I'm still wondering about the overall_best_*.* outputs - are these the
>> really final output, or do we go for cycle_best_3.* series?
The overall_best_xxx files are copied from the cycle_best_xxx files which
are copied from the original files, all of which are in the TEMP0/

Thanks for pointing out that the difference coefficients are not present
in the autobuild map file.  I will fix the output to have the original
refinement map file available.

All the best,
Tom T

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