Hi Jon, I would think that exptl_fobs_phases_freeR_flags_xx.mtz should have the labels you want. (You don't want to use overall_best_denmod_map_coeffs.mtz in refinement, only to create maps.) For example: phenix.mtz.dump exptl_fobs_phases_freeR_flags_2.mtz Processing: exptl_fobs_phases_freeR_flags_2.mtz Title: Resolve mtz file Space group symbol from file: C2 Space group number from file: 5 Space group from matrices: C 1 2 1 (No. 5) Point group symbol from file: PG2 Number of crystals: 2 Number of Miller indices: 2692 Resolution range: 21.3298 2.59408 History: From CCP4 20/ 3/2010 19:45:21 Crystal 1: Name: HKL_base Project: HKL_base Id: 1 Unit cell: (76.08, 27.97, 42.36, 90, 103.2, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 3 label #valid %valid min max type H 2692 100.00% -28.00 27.00 H: index h,k,l K 2692 100.00% 0.00 10.00 H: index h,k,l L 2692 100.00% 0.00 15.00 H: index h,k,l Crystal 2: Name: crystal Project: project Id: 2 Unit cell: (76.08, 27.97, 42.36, 90, 103.2, 90) Number of datasets: 1 Dataset 1: Name: dataset Id: 1 Wavelength: 1 Number of columns: 10 label #valid %valid min max type FP 2692 100.00% 11.41 902.45 F: amplitude SIGFP 2692 100.00% 0.86 17.94 Q: standard deviation PHIM 2692 100.00% -179.89 180.00 P: phase angle in degrees FOMM 2692 100.00% 0.00 1.00 W: weight (of some sort) HLAM 2692 100.00% -14.26 13.84 A: phase probability coefficients (Hendrickson/Lattman) HLBM 2692 100.00% -14.36 10.86 A: phase probability coefficients (Hendrickson/Lattman) HLCM 2692 100.00% -2.83 4.81 A: phase probability coefficients (Hendrickson/Lattman) HLDM 2692 100.00% -4.71 3.77 A: phase probability coefficients (Hendrickson/Lattman) FreeR_flag 2692 100.00% 0.00 1.00 I: integer FC 2692 100.00% 0.00 0.00 F: amplitude I hope that helps! Please let me know if not. -Tom T
Hello all,
I used AutoSol to generate a model from my Se-Met crystal. I then used this output model, overall_best.pdb, for AutoBuild1 in which I extended the data to include a set of native data. At this point I took the exptl_fobs_phases_freeR_flags.mtz output and used it with a different model that I believe to be accurate to carry out AutoBuild2. The problem I'm having is that I can't run Refmac/Phenix refinements on the output from AutoBuild2: overall_best.pdb and overall_best_denmod_map_coeffs.mtz. Both pieces of software say the FreeR labels are missing although in the AutoBuild2 output PDB there is a FreeR test set count of ~2,000. When I list all labels in Refmac I see:
F FP P PHIM W FOMM
Using these labels doesn't work for refinement. I used default settings for AutoSol/AutoBuild except for the number of Se-Met sites and of course the f' and f'' etc. I'm assuming the problem is with the MTZ but I'm not sure where to troubleshoot. Does anyone have any thoughts?
Thanks in advance, Jon _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb