Hi Ed,
So far I've only checked the phenix.refine output files (both mtz with map coefficients and calculated amplitudes).
phenix.refine uses the iotbx.mtz module I mentioned before. It definitely writes the HKL_base information. You can use phenix.mtz.dump to check. See below for an example. Let me know if you think it isn't right, but it has been this way for over five years. Ralf % phenix.mtz.dump tmp_refine_001_map_coeffs.mtz Processing: tmp_refine_001_map_coeffs.mtz Title: None Space group symbol from file: P21 Space group number from file: 4 Space group from matrices: P 1 21 1 (No. 4) Point group symbol from file: 2 Number of crystals: 2 Number of Miller indices: 553 Resolution range: 22.4416 1.80066 History: Date 2010-08-16 Time 18:29:14 PDT -0700 (1282008554.15 s)
file name: tmp_refine_001_map_coeffs.mtz Crystal 1: Name: HKL_base Project: HKL_base Id: 0 Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 0 Crystal 2: Name: crystal Project: project Id: 2 Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90) Number of datasets: 1 Dataset 1: Name: dataset Id: 1 Wavelength: 1 Number of columns: 9 label #valid %valid min max type H 553 100.00% -12.00 11.00 H: index h,k,l K 553 100.00% 0.00 2.00 H: index h,k,l L 553 100.00% 0.00 13.00 H: index h,k,l 2FOFCWT 553 100.00% 0.01 97.89 F: amplitude PH2FOFCWT 553 100.00% -179.41 180.00 P: phase angle in degrees 2FOFCWT_no_fill 494 89.33% 0.05 76.28 F: amplitude PH2FOFCWT_no_fill 494 89.33% -178.65 180.00 P: phase angle in degrees FOFCWT 494 89.33% 0.04 37.99 F: amplitude PHFOFCWT 494 89.33% -177.51 180.00 P: phase angle in degrees