[phenixbb] Confused by the output from Phenix autobuild jobs

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Nov 30 03:24:59 PST 2009

Hi Serah,

I have fixed the output of phenix.autobuild so that the phenix.refine map
coefficients file is available in the AutoBuild_run_xx_/ directory after
the run is finished, and so that the list of output files at the end of
your log file lists it correctly.  This is available in versions of phenix
starting with version 1.5-dev-242 (today's version).

Let me know of any problems!

All the best,
Tom T

>> 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 \
>>   AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz
>> 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/
>> subdirectory.
>> 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb

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