Running the Individual Steps: Small Molecule -------------------------------------------- FIXME write this section too, and in each section detail the available parameters. Guess it would also be rather nice to write about the available parameters, and :samp:`dials.parameters`. For this example will process some small-molecule data (sugar) to really demonstrate how the command-line options work. Import ^^^^^^ The first stage of step-by-step DIALS processing is to import the data - all that happens here is that the image headers are read, and a file describing their contents (:samp:`datablock.json`) is written. It's worth noting that if this file is changed subsequent processing can use this. :: dials.import ~/data/sugar/15_n_120K_1_00*cbf The output just describes what the software understands of the images it was passed - not very interesting but useful to make sure it all makes sense. :: -------------------------------------------------------------------------------- DataBlock 0 format: num images: 645 num sweeps: 1 num stills: 0 -------------------------------------------------------------------------------- Writing datablocks to datablock.json Find Spots ^^^^^^^^^^ The first "real" task in any DIALS processing will be the spot finding - while there are plenty of options the defaults often seem to do sensible things. :: dials.find_spots datablock.json This will just report the number of spots found - guess we could probably write some more interesting output. :: Configuring spot finder from input parameters -------------------------------------------------------------------------------- Finding strong spots in imageset 0 -------------------------------------------------------------------------------- Finding spots in image 0 to 645... Extracted strong pixels from images.......................................24.35s Merged 8 pixel lists with 34901 pixels.....................................0.00s Extracted 6951 spots.......................................................0.09s Calculated 6951 spot centroids.............................................0.09s Calculated 6951 spot intensities...........................................0.01s Filtered 1448 spots by number of pixels....................................0.00s Filtered 1374 spots by peak-centroid distance..............................0.00s -------------------------------------------------------------------------------- Saved 1374 reflections to strong.pickle....................................0.01s Total time: 26.5041749477 Indexing ^^^^^^^^ Here we will use a bunch more options to properly index the data, as the unit cell from sucrose is very small! Method of fft1d corresponds to the 1D FFT indexing rather than the 3D FFT default, the grid spacing clues just determine how the indexing is done. N.B. the defaults are configured for macromolecular crystallography. :: dials.index method=fft1d reciprocal_space_grid.d_min=1 refinement_protocol.d_min_start=1 datablock.json strong.pickle max_cell=20 The output for this is rather verbose: FIXME perhaps I should abbreviate it some? :: reference { detector = None beam = None } discover_better_experimental_model = False min_cell = 20 max_cell = 20 reciprocal_space_grid { n_points = 256 d_min = 1 } sigma_phi_deg = None b_iso = 200 rmsd_cutoff = 15 scan_range = None known_symmetry { space_group = None unit_cell = None relative_length_tolerance = 0.1 absolute_angle_tolerance = 10 } optimise_initial_basis_vectors = False debug = False debug_plots = False show_timing = False refinement { parameterisation { beam { fix = all *in_spindle_plane out_spindle_plane fix_list = None } crystal { fix = all cell orientation cell_fix_list = None orientation_fix_list = None scan_varying = False num_intervals = *fixed_width absolute interval_width_degrees = 36.0 absolute_num_intervals = 5 } detector { panels = *automatic single multiple hierarchical hierarchy_level = 0 fix = all position orientation fix_list = None } } refinery { engine = SimpleLBFGS LBFGScurvs GaussNewtonIterations *LevMarIterations track_step = False track_gradient = False track_parameter_correlation = False log = None max_iterations = None } target { rmsd_cutoff = *fraction_of_bin_size absolute bin_size_fraction = 0.33333 absolute_cutoffs = None } reflections { reflections_per_degree = 50 minimum_sample_size = 1000 maximum_number_of_reflections = None use_all_reflections = False random_seed = 42 minimum_number_of_reflections = 20 close_to_spindle_cutoff = 0.1 do_outlier_rejection = False iqr_multiplier = 1.5 } } refinement_protocol { weight_outlier_n_sigma = 5 n_macro_cycles = 3 d_min_step = 1.0 d_min_start = 1 d_min_final = None verbosity = 1 outlier_rejection { maximum_spot_error = None hkl_tolerance = 0.3 } } method = fft3d *fft1d real_space_grid_search multiple_lattice_search { cluster_analysis_search = False recycle_unindexed_reflections = False recycle_unindexed_reflections_cutoff = 0.1 max_lattices = None cluster_analysis { method = *dbscan hcluster hcluster { linkage { method = *ward metric = *euclidean } cutoff = 15 cutoff_criterion = *distance inconsistent } dbscan { eps = 0.05 min_samples = 30 } min_cluster_size = 20 intersection_union_ratio_cutoff = 0.4 } } Detector: Panel: pixel_size:{0.172,0.172} image_size: {487,619} trusted_range: {-1,243592} fast_axis: {1,0,0} slow_axis: {0,-0.866025,-0.5} origin: {-41.05,87.8104,-47.4522} Scan: image range: {1,645} oscillation: {-92,0.2} Goniometer: Rotation axis: {1,-3.17778e-14,1.59583e-14} Fixed rotation: {0.661179,0.0297045,0.74964,-0.284305,-0.914768,0.287003,0.694272,-0.402887,-0.59638} Beam: wavelength: 0.6889 sample to source direction : {0,0,1} divergence: 0 sigma divergence: 0 polarization normal: {0,1,0} polarization fraction: 0.8 model 1 (136 reflections): Crystal: Unit cell: (7.493, 8.354, 10.337, 89.635, 77.719, 88.128) Space group: P 1 U matrix: {{ 0.5248, -0.3912, 0.7560}, {-0.2594, -0.9194, -0.2956}, { 0.8107, -0.0410, -0.5840}} B matrix: {{ 0.1335, 0.0000, 0.0000}, {-0.0044, 0.1198, 0.0000}, {-0.0291, 0.0001, 0.0990}} A = UB: {{ 0.0498, -0.0468, 0.0749}, {-0.0220, -0.1101, -0.0293}, { 0.1254, -0.0050, -0.0578}} 801 unindexed reflections ################################################################################ Starting refinement (macro-cycle 1) ################################################################################ Running refinement ------------------ 0 1 2 3 4 5 6 7 8 9 10 11 Refinement steps ---------------- Step Nref Objective RMSD_X RMSD_Y RMSD_Phi 0 132 47422 0.4368 1.9379 0.024119 1 132 6910.7 0.36193 0.3461 0.01491 2 132 5063.1 0.34305 0.33002 0.012053 3 132 3846.4 0.32599 0.32141 0.009753 4 132 3396 0.31899 0.32687 0.0086288 5 132 3313.8 0.31916 0.3268 0.0084046 6 132 3293.2 0.32082 0.32416 0.0083628 7 132 3270.3 0.32025 0.32331 0.008318 8 132 3251.2 0.31897 0.32334 0.0082794 9 132 3246.1 0.31816 0.32369 0.0082696 10 132 3245.8 0.31794 0.32383 0.0082692 11 132 3245.8 0.31792 0.32384 0.0082692 RMSD no longer decreasing Increasing resolution to 0.0 Angstrom model 1 (1034 reflections): Crystal: Unit cell: (7.653, 8.586, 10.666, 89.631, 77.289, 89.852) Space group: P 1 U matrix: {{ 0.5443, -0.3908, 0.7423}, {-0.2534, -0.9201, -0.2986}, { 0.7997, -0.0255, -0.5999}} B matrix: {{ 0.1307, 0.0000, 0.0000}, {-0.0003, 0.1165, 0.0000}, {-0.0295, -0.0007, 0.0961}} A = UB: {{ 0.0494, -0.0460, 0.0713}, {-0.0240, -0.1070, -0.0287}, { 0.1222, -0.0026, -0.0577}} 62 unindexed reflections ################################################################################ Starting refinement (macro-cycle 2) ################################################################################ Running refinement ------------------ 0 1 2 3 4 5 6 7 8 9 10 Refinement steps ---------------- Step Nref Objective RMSD_X RMSD_Y RMSD_Phi 0 1027 50906 0.46797 0.43965 0.011741 1 1027 31234 0.30073 0.31112 0.010643 2 1027 27298 0.25668 0.27272 0.010466 3 1027 23548 0.2175 0.21235 0.010339 4 1027 21868 0.20436 0.17651 0.010241 5 1027 21595 0.20583 0.17004 0.010195 6 1027 21456 0.2056 0.16845 0.010167 7 1027 21368 0.20484 0.16744 0.010154 8 1027 21353 0.20449 0.16708 0.010154 9 1027 21352 0.20442 0.16702 0.010155 10 1027 21352 0.20442 0.16701 0.010155 RMSD no longer decreasing Final refined crystal models: model 1 (1034 reflections): Crystal: Unit cell: (7.743, 8.707, 10.817, 90.180, 76.968, 90.281) Space group: P 1 U matrix: {{ 0.5416, -0.3876, 0.7460}, {-0.2449, -0.9216, -0.3011}, { 0.8042, -0.0196, -0.5940}} B matrix: {{ 0.1291, 0.0000, 0.0000}, { 0.0006, 0.1148, 0.0000}, {-0.0299, 0.0002, 0.0949}} A = UB: {{ 0.0474, -0.0443, 0.0708}, {-0.0232, -0.1059, -0.0286}, { 0.1216, -0.0024, -0.0564}} usr+sys time: 20.34 seconds, ticks: 99507393, micro-seconds/tick: 0.204 wall clock time: 20.48 seconds Refinement ^^^^^^^^^^ Although the model is already refined in indexing we can also add a refineent step in here to allow e.g. scan varying refinement (though with this data we are unlikely to really have enough measurements to do this!) :: dials.refine experiments.json indexed.pickle This one on the other hand would probably stand to be *more* verbose! :: Configuring refiner Performing refinement Saving refined experiments to refined_experiments.json Integration ^^^^^^^^^^^ After refinement is complete integration may proceed - though in this example it failed so this is not a great example! :: %%%FIXME make command line right! dials.integrate refined_experiments.json FIXME ADD IN HERE RESULTS Exporting as MTZ ^^^^^^^^^^^^^^^^ :: FIXME ADD IN HERE EXPORT STUFF