Re: [phenixbb] Confused by the output from Phenix autobuild jobs
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
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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (1)
-
Thomas C. Terwilliger