question about rfree flag transfer
Hi, I have built a model against a 3.7A data set by AutoBuild. The resulting model is overall_best.pdb. The data with the rfree test flags is exptl_fobs_phases_freeR_flags.mtz Later on, I got a 3.4A data, which is isomorphous with the 3.7A data. Now I want to transfer the rfree flag from the 3.7A to 3.4A data for refinement. I know one strategy if the data file is in CNS format. That is, use DATAMAN to transfer the flags and generate new test set flags in the high resolution range: 3.7-3.4A. However, when I convert the format by phenix.reflection_file_converter, it fails: phenix.reflection_file_converter exptl_fobs_phases_freeR_flags.mtz --cns=exptl_fobs_phases_freeR_flags.cv --label="PHIM" --label="FP,SIGFP" --label="FOMM" --label="FreeR_flag" --label="FC" However, the resulting data does not have any FP, SIGFP, and FreeR flags. { file: exptl_fobs_phases_freeR_flags.cv.cns } { sg=C2 a=175.385 b=102.472 c=92.057 alpha=90 beta=111.312 gamma=90 } { source of data: exptl_fobs_phases_freeR_flags.mtz:FC } NREFlections=15307 ANOMalous=FALSe DECLare NAME=DATA DOMAin=RECIprocal TYPE=REAL END INDEx 0 0 5 DATA= 0 INDEx 0 0 7 DATA= 0 INDEx 0 0 8 DATA= 0 INDEx 0 0 9 DATA= 0 INDEx 0 0 10 DATA= 0 INDEx 0 0 11 DATA= 0 INDEx 0 0 12 DATA= 0 INDEx 0 0 13 DATA= 0 I also tried mtz2various in CCP4i, the resulting hkl file does not have rfree flags at all. Does anyone know who to convert the exptl_fobs_phases_freeR_flags.mtz into cns format or simple transfer the flags by phenix?
On Sep 23, 2009, at 3:01 PM, crystallogrphy wrote:
I know one strategy if the data file is in CNS format. That is, use DATAMAN to transfer the flags and generate new test set flags in the high resolution range: 3.7-3.4A. However, when I convert the format by phenix.reflection_file_converter, it fails: phenix.reflection_file_converter exptl_fobs_phases_freeR_flags.mtz -- cns=exptl_fobs_phases_freeR_flags.cv --label="PHIM" -- label="FP,SIGFP" --label="FOMM" --label="FreeR_flag" --label="FC"
I also tried mtz2various in CCP4i, the resulting hkl file does not have rfree flags at all.
Does anyone know who to convert the exptl_fobs_phases_freeR_flags.mtz into cns format or simple transfer the flags by phenix?
In theory: phenix.reflection_file_editor In practice: it will work best if you just use MTZ format for everything. You will need at least the most recent released installer (1.4-162) for this; there may still be some bugs in that version of the program. If it doesn't work for your files, I'll see if I can fix it - I'd like to make it as robust as possible. -Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
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Nathaniel Echols