Dear phenix developers, 1) I would like to do paired refinement using the phenix refine gui. It would be nice if you could confirm if my settings are ok, or if there are still some settings in the background which I overlooked, because we see small changes in R and Rfree. a, I added the model refined at higher resolution (e.g. 1.5A) and the mtz file cut at CC (e.g.1.5A) in the "Input data" tab, and set High resolution cutoff in "X-ray data and experimental phases" box to (e.g. 1.8A) In the refinement setting strategy tab I uncheck everything and set Number of cycles = 1. In "other options" I uncheck everything too. b, Alternatively adding a file to the input data with } xray_data { file_name = "/XYZ.mtz" labels = "FP,SIGFP" high_resolution = 1.8 low_resolution = None outliers_rejection = True french_wilson_scale = True french_wilson { max_bins = 60 min_bin_size = 40 } refine { strategy = none sites { individual = None torsion_angles = None rigid_body = None } main { bulk_solvent_and_scale = True apply_overall_isotropic_scale_to_adp = True fix_rotamers = False flip_peptides = False nqh_flips = False use_molprobity = True simulated_annealing = False simulated_annealing_torsion = False ordered_solvent = False } should also do the same or have I overlooking something. 2. For whatever reason I would like to do that (molprobity) - can I (and how can I do this) add the command line commands also in the gui? 3. In december 2012 there was a discussion about weak data and refinement. I would like to know if there are new data available showing that "Whether the benefit they describe is considered cosmetic or non-trivial,....." 4. Additionally could one short comment on what phenix is doing with strong (weak) reflections marked as aliens in XDS. 5. According to the supplementary of P. Andrew Karplus, Kay Diederichs "Linking Crystallographic Model and Data Quality" I would like to do anisotropic refinement, with additional options "ordered_solvent.new_solvent=anisotropic adp.individual.anisotropic="not element H" fix_rotamers=True". Putting this in a file is enough? main { bulk_solvent_and_scale = True apply_overall_isotropic_scale_to_adp = True fix_rotamers = True flip_peptides = False nqh_flips = False use_molprobity = True simulated_annealing = False simulated_annealing_torsion = False ordered_solvent = True } refinement { refine { adp { individual { isotropic = none anisotropic = not element H } } } } The "problem" mentioned in phenix documentation is not a problem with the gui? it is a good idea to constantly monitor the existing solvent molecules and check for new ones by using ordered_solvent=true keyword. If it's decided to refine waters with anisotropic ADP then make sure that the newly added ones are also anisotropic; useordered_solvent.new_solvent=anisotropic (default is isotropic). Thanks in advance and best regards, Georg.