Multi-lattice Tutorial ================= Introduction ------------ The following example uses semi-synthetic multi-lattice trypsin datasets collected using beamline I04 at Diamond Light Source which is available for download from |semisynthetic|. This tutorial uses one of the 2-lattice datasets which are contained in the file `semisynthetic_multilattice_data_2.tar.bz2`_. .. _semisynthetic_multilattice_data_2.tar.bz2: https://zenodo.org/record/10820/files/semisynthetic_multilattice_data_2.tar.bz2 .. |semisynthetic| image:: https://zenodo.org/badge/doi/10.5281/zenodo.10820.png :target: http://dx.doi.org/10.5281/zenodo.10820 A complete example script can be found :download:`here<../user-tutorial/multi_lattice_tutorial.sh>`, which can be run as follows:: ./multi_latice_tutorial.sh /path/to/semisynthetic_multilattice_data 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 semisynthetic_multilattice_data/2/ag/trp_ag_*.cbf The output just describes what the software understands of the images it was passed, in this case one sweep of data containing 100 images. :: The following parameters have been modified: input { datablock = } -------------------------------------------------------------------------------- DataBlock 0 format: num images: 100 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. Here we tweak the minimum spot size (min_spot_size=3) and use multiple processors to speed up the spot-finding (nproc=4). :: dials.find_spots datablock.json min_spot_size=3 nproc=4 This will just report the number of spots found. :: Writing datablocks to datablock.json The following parameters have been modified: spotfinder { mp { nproc = 4 } filter { min_spot_size = 3 } } input { datablock = datablock.json } Configuring spot finder from input parameters -------------------------------------------------------------------------------- Finding strong spots in imageset 0 -------------------------------------------------------------------------------- Finding spots in image 0 to 100... Extracting strong pixels from images (may take a while) Extracted strong pixels from images Merging 4 pixel lists Merged 4 pixel lists with 763338 pixels Extracting spots Extracted 68439 spots Calculating 68439 spot centroids Calculated 68439 spot centroids Calculating 68439 spot intensities Calculated 68439 spot intensities Filtering 68439 spots by number of pixels Filtered 40212 spots by number of pixels Filtering 40212 spots by peak-centroid distance Filtered 38341 spots by peak-centroid distance -------------------------------------------------------------------------------- Saving 38341 reflections to strong.pickle Saved 38341 reflections to strong.pickle Indexing ^^^^^^^^ The next step will be indexing of the strong spots. By default only one lattice is searched for, but if there are sufficient unindexed reflections remaining after indexing the first lattice, we can switch on indexing of multiple lattices using the parameter max_lattices=2 (e.g.):: dials.index datablock.json strong.pickle \ max_lattices=2 \ refinement.reflections.use_all_reflections=true \ maximum_spot_error=3 maximum_phi_error=2 :: The following parameters have been modified: indexing { refinement_protocol { outlier_rejection { maximum_spot_error = 3 maximum_phi_error = 2 } } multiple_lattice_search { max_lattices = 2 } } refinement { reflections { use_all_reflections = true } } input { datablock = datablock.json reflections = strong.pickle } ... RMSDs by experiment ------------------- ---------------------------------------------- | Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z | | | | (px) | (px) | (images) | ---------------------------------------------- | 0 | 16344 | 0.51285 | 0.41374 | 0.79065 | | 1 | 16594 | 0.37963 | 0.3806 | 0.78624 | ---------------------------------------------- Finish searching for more lattices: 3834 unindexed reflections remaining. Rotation matrix to transform crystal 1 to crystal 2 {{0.973, -0.159, -0.170}, {-0.069, -0.895, 0.441}, {-0.222, -0.417, -0.881}} Euler angles (xyz): -153.44, -9.77, 9.28 Final refined crystal models: model 1 (17355 reflections): Crystal: Unit cell: (54.116, 58.294, 66.530, 90.010, 90.036, 90.023) Space group: P 1 U matrix: {{-0.1871, 0.7625, 0.6194}, {-0.0431, 0.6235, -0.7806}, {-0.9814, -0.1727, -0.0838}} B matrix: {{ 0.0185, 0.0000, 0.0000}, { 0.0000, 0.0172, 0.0000}, { 0.0000, 0.0000, 0.0150}} A = UB: {{-0.0034, 0.0131, 0.0093}, {-0.0008, 0.0107, -0.0117}, {-0.0181, -0.0030, -0.0013}} model 2 (17758 reflections): Crystal: Unit cell: (54.134, 58.298, 66.538, 89.995, 89.992, 89.969) Space group: P 1 U matrix: {{-0.0085, 0.6719, 0.7406}, {-0.3810, -0.6870, 0.6188}, { 0.9245, -0.2769, 0.2618}} B matrix: {{ 0.0185, 0.0000, 0.0000}, {-0.0000, 0.0172, 0.0000}, {-0.0000, -0.0000, 0.0150}} A = UB: {{-0.0002, 0.0115, 0.0111}, {-0.0070, -0.0118, 0.0093}, { 0.0171, -0.0048, 0.0039}} Next we run :doc:`dials.refine_bravais_settings ` refining each indexing solution (separately) in all Bravais settings consistent with the indexed unit cell. In this example we would continue processing using bravais_setting_5.json, i.e. solution number 5. :: dials.refine_bravais_settings experiments.json indexed.pickle crystal_id=0 dials.refine_bravais_settings experiments.json indexed.pickle crystal_id=1 gives a table containing the metric fit, rmsds (in mm) and unit cell for each Bravais setting... :: ------------------------------------------------------------------------------------------------------------ Solution Metric fit rmsd #spots crystal_system unit_cell volume cb_op ------------------------------------------------------------------------------------------------------------ 9 4.2577 dg 1.988 1000 tetragonal tP 60.17 60.17 69.10 90.00 90.00 90.00 250161 a,b,c 8 4.2577 dg 1.982 1000 orthorhombic oC 84.45 85.33 69.01 90.00 90.00 90.00 497254 a+b,-a+b,c 7 4.2577 dg 1.950 1000 monoclinic mC 85.47 84.17 68.98 90.00 89.85 90.00 496214 a-b,a+b,c 6 4.2576 dg 1.948 1000 monoclinic mC 84.43 85.30 68.99 90.00 89.97 90.00 496845 a+b,-a+b,c 5 0.0432 dg 0.135 1000 orthorhombic oP 54.16 58.30 66.54 90.00 90.00 90.00 210119 a,b,c 4 0.0432 dg 0.135 1000 monoclinic mP 58.31 54.16 66.54 90.00 90.01 90.00 210136 -b,-a,-c 3 0.0376 dg 0.135 1000 monoclinic mP 54.16 66.54 58.30 90.00 90.03 90.00 210093 -a,-c,-b 2 0.0255 dg 0.136 1000 monoclinic mP 54.15 58.30 66.52 90.00 90.06 90.00 209989 a,b,c 1 0.0000 dg 0.134 1000 triclinic aP 54.15 58.29 66.52 90.02 90.07 90.04 209985 a,b,c ------------------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------------ Solution Metric fit rmsd #spots crystal_system unit_cell volume cb_op ------------------------------------------------------------------------------------------------------------ 9 4.2423 dg 2.228 1000 tetragonal tP 59.39 59.39 68.39 90.00 90.00 90.00 241196 a,b,c 8 4.2423 dg 2.208 1000 orthorhombic oC 84.64 83.94 68.47 90.00 90.00 90.00 486463 a-b,a+b,c 7 4.2423 dg 1.930 1000 monoclinic mC 82.03 83.17 67.01 90.00 91.78 90.00 456951 a-b,a+b,c 6 4.2423 dg 1.797 1000 monoclinic mC 83.47 82.31 67.96 90.00 88.86 90.00 466784 a+b,-a+b,c 5 0.0317 dg 0.133 1000 orthorhombic oP 54.09 58.32 66.53 90.00 90.00 90.00 209871 a,b,c 4 0.0317 dg 0.133 1000 monoclinic mP 58.32 54.09 66.53 90.00 90.00 90.00 209868 -b,-a,-c 3 0.0311 dg 0.133 1000 monoclinic mP 54.07 58.31 66.50 90.00 90.06 90.00 209664 a,b,c 2 0.0093 dg 0.136 1000 monoclinic mP 54.11 66.54 58.33 90.00 90.04 90.00 210020 -a,-c,-b 1 0.0000 dg 0.138 1000 triclinic aP 54.09 58.33 66.50 89.99 90.07 90.05 209814 a,b,c ------------------------------------------------------------------------------------------------------------ Now we re-run the indexing, this time imposing the lattice constraints for the chosen Bravais setting, in this case number 5, i.e. oP, or point group P222. :: dials.index datablock.json strong.pickle \ max_lattices=2 \ refinement.reflections.use_all_reflections=true \ maximum_spot_error=3 maximum_phi_error=2 \ space_group=P222 :: The following parameters have been modified: indexing { known_symmetry { space_group = P222 } refinement_protocol { outlier_rejection { maximum_spot_error = 3 maximum_phi_error = 2 } } multiple_lattice_search { max_lattices = 2 } } refinement { reflections { use_all_reflections = true } } input { datablock = datablock.json reflections = strong.pickle } ... RMSDs by experiment ------------------- ---------------------------------------------- | Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z | | | | (px) | (px) | (images) | ---------------------------------------------- | 0 | 17030 | 0.52795 | 0.42652 | 0.78267 | | 1 | 17351 | 0.41002 | 0.39527 | 0.79255 | ---------------------------------------------- Finish searching for more lattices: 3834 unindexed reflections remaining. Rotation matrix to transform crystal 1 to crystal 2 {{0.052, 0.997, -0.063}, {-0.978, 0.038, -0.204}, {-0.201, 0.072, 0.977}} Euler angles (xyz): 11.79, -3.60, -87.01 Final refined crystal models: model 1 (17356 reflections): Crystal: Unit cell: (54.115, 58.298, 66.535, 90.000, 90.000, 90.000) Space group: P 2 2 2 U matrix: {{-0.1865, 0.7626, 0.6193}, {-0.0431, 0.6234, -0.7807}, {-0.9815, -0.1723, -0.0834}} B matrix: {{ 0.0185, 0.0000, 0.0000}, {-0.0000, 0.0172, 0.0000}, {-0.0000, 0.0000, 0.0150}} A = UB: {{-0.0034, 0.0131, 0.0093}, {-0.0008, 0.0107, -0.0117}, {-0.0181, -0.0030, -0.0013}} model 2 (17757 reflections): Crystal: Unit cell: (54.133, 58.311, 66.533, 90.000, 90.000, 90.000) Space group: P 2 2 2 U matrix: {{-0.0090, 0.6719, 0.7406}, {-0.3809, -0.6871, 0.6187}, { 0.9246, -0.2766, 0.2621}} B matrix: {{ 0.0185, 0.0000, 0.0000}, {-0.0000, 0.0171, 0.0000}, {-0.0000, 0.0000, 0.0150}} A = UB: {{-0.0002, 0.0115, 0.0111}, {-0.0070, -0.0118, 0.0093}, { 0.0171, -0.0047, 0.0039}} Refinement ^^^^^^^^^^ Although the models are already refined in indexing we can also add a refinement step in here to allow e.g. scan varying refinement. :: dials.refine experiments.json indexed.pickle \ use_all_reflections=True scan_varying=True \ outlier.algorithm=tukey :: The following parameters have been modified: refinement { parameterisation { crystal { scan_varying = True } } reflections { use_all_reflections = True outlier { algorithm = null *tukey } } } input { experiments = experiments.json reflections = indexed.pickle } Configuring refiner Summary statistics for observations matched to predictions: ------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | ------------------------------------------------------------------------- | Xc - Xo (mm) | -0.9823 | -0.0517 | 0.002165 | 0.04972 | 0.6267 | | Yc - Yo (mm) | -2.051 | -0.03828 | 0.0007268 | 0.03696 | 2.383 | | Phic - Phio (deg) | -4.79 | -0.01656 | 0.002315 | 0.0159 | 4.187 | | X weights | 126.2 | 134.4 | 134.9 | 135.1 | 135.2 | | Y weights | 125.4 | 134.5 | 135 | 135.2 | 135.2 | | Phi weights | 379.4 | 398.9 | 399.6 | 399.9 | 400 | ------------------------------------------------------------------------- Summary statistics for observations matched to predictions: -------------------------------------------------------------------------- | | Min | Q1 | Med | Q3 | Max | -------------------------------------------------------------------------- | Xc - Xo (mm) | -0.2037 | -0.04754 | 0.003321 | 0.04794 | 0.2018 | | Yc - Yo (mm) | -0.1511 | -0.03304 | 0.002045 | 0.03517 | 0.1497 | | Phic - Phio (deg) | -0.06525 | -0.01247 | 0.002878 | 0.01467 | 0.06455 | | X weights | 126.5 | 134.5 | 134.9 | 135.1 | 135.2 | | Y weights | 125.4 | 134.6 | 135 | 135.2 | 135.2 | | Phi weights | 381.1 | 399 | 399.6 | 399.9 | 400 | -------------------------------------------------------------------------- Performing refinement Running refinement ------------------ 0 1 2 3 4 5 6 Refinement steps ---------------- ------------------------------------------------- | Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi | | | | (mm) | (mm) | (deg) | ------------------------------------------------- | 0 | 30214 | 0.07155 | 0.051119 | 0.022657 | | 1 | 30214 | 0.07135 | 0.050939 | 0.022084 | | 2 | 30214 | 0.071261 | 0.050932 | 0.021906 | | 3 | 30214 | 0.071173 | 0.050916 | 0.021827 | | 4 | 30214 | 0.071139 | 0.05092 | 0.02178 | | 5 | 30214 | 0.071134 | 0.050924 | 0.02177 | | 6 | 30214 | 0.071133 | 0.050925 | 0.021769 | ------------------------------------------------- RMSD no longer decreasing RMSDs by experiment ------------------- ---------------------------------------------- | Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z | | | | (px) | (px) | (images) | ---------------------------------------------- | 0 | 14739 | 0.46827 | 0.28366 | 0.22357 | | 1 | 15475 | 0.35367 | 0.30743 | 0.21195 | ---------------------------------------------- Saving refined experiments to refined_experiments.json Integration ^^^^^^^^^^^ After the refinement is done the next step is integration, which is performed by the program :doc:`dials.integrate `. :: dials.integrate refined_experiments.json indexed.pickle This program outputs a lot of information as integration progresses, concluding with a summary of the integration results. :: ================================================================================ Summary of integration results for experiment 0 Summary of integration results as a function of image number -------------------------------------------------------------------------------- Image | # full | # part | # sum | # prf | | | | | | | | | | (sum) | (prf) | -------------------------------------------------------------------------------- 0 | 315 | 1202 | 1517 | 1047 | 18.20 | 35.81 | 53.38 | 0.64 1 | 563 | 1204 | 1767 | 1282 | 18.18 | 35.19 | 51.10 | 0.65 2 | 791 | 1204 | 1995 | 1496 | 18.22 | 34.96 | 49.89 | 0.65 3 | 1010 | 1205 | 2215 | 1696 | 18.16 | 34.05 | 48.05 | 0.65 4 | 1245 | 1182 | 2427 | 1898 | 18.12 | 33.80 | 47.20 | 0.66 5 | 1464 | 1042 | 2506 | 2037 | 18.11 | 33.91 | 46.42 | 0.66 6 | 1691 | 887 | 2578 | 2164 | 18.01 | 33.83 | 45.41 | 0.66 7 | 1975 | 689 | 2664 | 2288 | 18.02 | 34.25 | 45.32 | 0.66 8 | 2105 | 560 | 2665 | 2325 | 17.99 | 34.15 | 44.75 | 0.66 9 | 2193 | 456 | 2649 | 2323 | 17.88 | 34.12 | 44.60 | 0.66 10 | 2250 | 396 | 2646 | 2332 | 17.69 | 33.83 | 44.03 | 0.65 11 | 2306 | 350 | 2656 | 2357 | 17.68 | 33.45 | 43.46 | 0.65 12 | 2379 | 306 | 2685 | 2394 | 17.77 | 33.58 | 43.53 | 0.65 13 | 2381 | 283 | 2664 | 2385 | 17.83 | 34.23 | 44.21 | 0.65 14 | 2425 | 263 | 2688 | 2424 | 17.98 | 35.23 | 45.06 | 0.65 15 | 2415 | 244 | 2659 | 2400 | 17.91 | 34.84 | 44.68 | 0.65 16 | 2422 | 231 | 2653 | 2390 | 17.83 | 34.75 | 44.49 | 0.65 17 | 2436 | 217 | 2653 | 2401 | 17.77 | 33.49 | 42.78 | 0.64 18 | 2471 | 199 | 2670 | 2425 | 17.74 | 33.79 | 42.96 | 0.64 19 | 2492 | 195 | 2687 | 2452 | 17.79 | 34.27 | 43.41 | 0.64 20 | 2495 | 182 | 2677 | 2444 | 17.91 | 34.67 | 43.83 | 0.65 21 | 2533 | 171 | 2704 | 2478 | 17.98 | 34.48 | 43.66 | 0.64 22 | 2553 | 162 | 2715 | 2483 | 17.97 | 34.32 | 43.48 | 0.64 23 | 2614 | 151 | 2765 | 2537 | 17.90 | 33.70 | 42.91 | 0.65 24 | 2608 | 144 | 2752 | 2528 | 17.84 | 33.06 | 42.21 | 0.65 25 | 2620 | 140 | 2760 | 2535 | 17.83 | 33.67 | 42.84 | 0.65 26 | 2605 | 143 | 2748 | 2525 | 17.68 | 33.45 | 42.54 | 0.64 27 | 2624 | 145 | 2769 | 2552 | 17.79 | 34.59 | 43.82 | 0.65 28 | 2594 | 140 | 2734 | 2521 | 17.81 | 34.78 | 44.06 | 0.65 29 | 2585 | 142 | 2727 | 2511 | 17.75 | 34.76 | 44.08 | 0.65 30 | 2560 | 134 | 2694 | 2483 | 17.86 | 35.42 | 44.76 | 0.64 31 | 2557 | 140 | 2697 | 2487 | 17.88 | 35.90 | 45.39 | 0.64 32 | 2589 | 142 | 2731 | 2516 | 17.79 | 35.91 | 45.40 | 0.64 33 | 2590 | 147 | 2737 | 2522 | 17.76 | 35.86 | 45.29 | 0.64 34 | 2627 | 145 | 2772 | 2553 | 17.94 | 36.56 | 46.03 | 0.64 35 | 2605 | 143 | 2748 | 2534 | 17.96 | 36.88 | 46.36 | 0.64 36 | 2618 | 140 | 2758 | 2541 | 17.98 | 37.18 | 46.66 | 0.64 37 | 2648 | 136 | 2784 | 2570 | 17.80 | 36.17 | 45.55 | 0.63 38 | 2649 | 133 | 2782 | 2561 | 17.84 | 36.68 | 46.28 | 0.63 39 | 2637 | 131 | 2768 | 2546 | 17.69 | 35.89 | 45.31 | 0.63 40 | 2624 | 129 | 2753 | 2537 | 17.75 | 36.46 | 45.98 | 0.63 41 | 2647 | 128 | 2775 | 2562 | 17.75 | 36.41 | 45.89 | 0.64 42 | 2616 | 126 | 2742 | 2535 | 17.68 | 36.67 | 46.19 | 0.63 43 | 2622 | 126 | 2748 | 2542 | 17.75 | 37.47 | 47.11 | 0.63 44 | 2619 | 123 | 2742 | 2532 | 17.86 | 37.15 | 46.89 | 0.64 45 | 2637 | 120 | 2757 | 2549 | 17.95 | 37.63 | 47.43 | 0.64 46 | 2632 | 121 | 2753 | 2548 | 17.96 | 37.85 | 47.64 | 0.64 47 | 2603 | 121 | 2724 | 2517 | 18.15 | 38.82 | 48.72 | 0.64 48 | 2623 | 122 | 2745 | 2538 | 18.14 | 38.62 | 48.28 | 0.64 49 | 2644 | 121 | 2765 | 2556 | 18.10 | 38.03 | 47.79 | 0.64 50 | 2653 | 121 | 2774 | 2567 | 18.04 | 37.25 | 46.84 | 0.64 51 | 2657 | 121 | 2778 | 2574 | 18.04 | 37.28 | 46.82 | 0.64 52 | 2664 | 121 | 2785 | 2578 | 17.91 | 37.54 | 47.13 | 0.64 53 | 2643 | 121 | 2764 | 2553 | 17.85 | 37.33 | 46.84 | 0.64 54 | 2631 | 122 | 2753 | 2546 | 17.88 | 37.62 | 47.16 | 0.64 55 | 2642 | 122 | 2764 | 2556 | 17.87 | 38.09 | 47.70 | 0.64 56 | 2651 | 122 | 2773 | 2557 | 17.95 | 37.98 | 47.73 | 0.64 57 | 2667 | 125 | 2792 | 2576 | 18.07 | 38.70 | 48.56 | 0.64 58 | 2665 | 128 | 2793 | 2572 | 18.05 | 39.47 | 49.44 | 0.64 59 | 2655 | 128 | 2783 | 2558 | 18.07 | 39.60 | 49.76 | 0.64 60 | 2628 | 129 | 2757 | 2539 | 18.23 | 40.19 | 50.45 | 0.64 61 | 2608 | 131 | 2739 | 2514 | 18.23 | 40.10 | 50.45 | 0.64 62 | 2630 | 133 | 2763 | 2541 | 18.11 | 39.59 | 49.74 | 0.64 63 | 2604 | 134 | 2738 | 2519 | 18.03 | 39.25 | 49.43 | 0.64 64 | 2594 | 134 | 2728 | 2512 | 18.11 | 39.51 | 49.80 | 0.64 65 | 2596 | 140 | 2736 | 2518 | 17.95 | 39.14 | 49.46 | 0.65 66 | 2559 | 138 | 2697 | 2480 | 17.85 | 38.71 | 49.00 | 0.64 67 | 2583 | 140 | 2723 | 2501 | 17.73 | 37.24 | 47.33 | 0.64 68 | 2604 | 146 | 2750 | 2552 | 17.72 | 35.66 | 44.99 | 0.63 69 | 2662 | 144 | 2806 | 2609 | 17.81 | 35.98 | 45.27 | 0.63 70 | 2616 | 149 | 2765 | 2567 | 17.78 | 36.38 | 45.66 | 0.63 71 | 2587 | 152 | 2739 | 2546 | 17.85 | 36.08 | 45.27 | 0.63 72 | 2588 | 155 | 2743 | 2547 | 17.93 | 36.68 | 45.91 | 0.63 73 | 2579 | 156 | 2735 | 2532 | 17.98 | 36.85 | 46.11 | 0.63 74 | 2583 | 158 | 2741 | 2540 | 17.95 | 37.26 | 46.51 | 0.63 75 | 2560 | 165 | 2725 | 2521 | 17.99 | 37.35 | 46.76 | 0.63 76 | 2571 | 167 | 2738 | 2535 | 18.05 | 37.62 | 47.15 | 0.64 77 | 2531 | 171 | 2702 | 2492 | 17.88 | 37.57 | 47.15 | 0.63 78 | 2530 | 175 | 2705 | 2479 | 17.77 | 37.02 | 46.63 | 0.63 79 | 2548 | 180 | 2728 | 2491 | 17.69 | 37.21 | 46.94 | 0.64 80 | 2572 | 182 | 2754 | 2513 | 17.71 | 36.75 | 46.50 | 0.64 81 | 2547 | 183 | 2730 | 2485 | 17.70 | 36.76 | 46.64 | 0.64 82 | 2521 | 188 | 2709 | 2460 | 17.66 | 36.00 | 45.75 | 0.64 83 | 2533 | 192 | 2725 | 2475 | 17.65 | 35.69 | 45.47 | 0.64 84 | 2517 | 200 | 2717 | 2460 | 17.70 | 35.44 | 45.42 | 0.64 85 | 2502 | 217 | 2719 | 2455 | 17.64 | 34.51 | 44.46 | 0.64 86 | 2483 | 233 | 2716 | 2449 | 17.54 | 34.35 | 44.41 | 0.65 87 | 2419 | 255 | 2674 | 2415 | 17.59 | 33.79 | 43.82 | 0.65 88 | 2361 | 300 | 2661 | 2389 | 17.45 | 33.56 | 43.64 | 0.65 89 | 2305 | 345 | 2650 | 2375 | 17.37 | 32.41 | 42.39 | 0.65 90 | 2259 | 405 | 2664 | 2371 | 17.36 | 32.19 | 42.34 | 0.65 91 | 2147 | 489 | 2636 | 2322 | 17.30 | 32.86 | 43.43 | 0.65 92 | 1984 | 598 | 2582 | 2243 | 17.24 | 33.04 | 44.01 | 0.66 93 | 1752 | 823 | 2575 | 2166 | 17.16 | 32.66 | 44.45 | 0.65 94 | 1506 | 997 | 2503 | 2037 | 17.13 | 32.52 | 44.95 | 0.65 95 | 1253 | 1139 | 2392 | 1879 | 17.11 | 31.90 | 44.96 | 0.65 96 | 1045 | 1178 | 2223 | 1700 | 17.14 | 31.51 | 45.01 | 0.65 97 | 805 | 1177 | 1982 | 1477 | 17.11 | 32.27 | 46.79 | 0.65 98 | 526 | 1176 | 1702 | 1212 | 16.92 | 31.56 | 46.93 | 0.64 99 | 300 | 1172 | 1472 | 997 | 16.90 | 31.33 | 48.07 | 0.64 -------------------------------------------------------------------------------- Summary of integration results binned by resolution --------------------------------------------------------------------------------------------------------- d min | d max | # full | # part | # over | # ice | # sum | # prf | | | | | | | | | | | | | (sum) | (prf) | --------------------------------------------------------------------------------------------------------- 1.06 | 1.08 | 31 | 3 | 0 | 0 | 34 | 18 | 4.43 | 2.05 | 3.65 | 0.34 1.08 | 1.10 | 124 | 18 | 0 | 0 | 142 | 110 | 4.81 | 2.18 | 3.55 | 0.35 1.10 | 1.12 | 204 | 18 | 0 | 0 | 222 | 180 | 5.32 | 2.27 | 3.66 | 0.34 1.12 | 1.14 | 326 | 30 | 0 | 0 | 356 | 295 | 5.84 | 2.79 | 4.69 | 0.41 1.14 | 1.17 | 433 | 39 | 0 | 0 | 472 | 396 | 6.37 | 3.18 | 5.66 | 0.45 1.17 | 1.20 | 578 | 65 | 0 | 0 | 643 | 548 | 7.00 | 3.48 | 5.70 | 0.45 1.20 | 1.23 | 779 | 82 | 0 | 0 | 861 | 732 | 7.70 | 3.89 | 6.33 | 0.48 1.23 | 1.26 | 1071 | 105 | 0 | 0 | 1176 | 1026 | 8.52 | 4.31 | 7.20 | 0.51 1.26 | 1.30 | 1334 | 148 | 0 | 0 | 1482 | 1311 | 9.21 | 4.75 | 7.60 | 0.52 1.30 | 1.34 | 1496 | 166 | 0 | 0 | 1662 | 1470 | 10.02 | 5.06 | 8.22 | 0.54 1.34 | 1.39 | 1411 | 177 | 0 | 0 | 1588 | 1450 | 10.76 | 5.98 | 9.40 | 0.57 1.39 | 1.44 | 1475 | 189 | 0 | 0 | 1664 | 1499 | 11.72 | 7.15 | 11.24 | 0.61 1.44 | 1.51 | 1478 | 188 | 0 | 0 | 1666 | 1507 | 12.84 | 9.47 | 14.62 | 0.66 1.51 | 1.59 | 1484 | 181 | 0 | 0 | 1665 | 1508 | 14.05 | 12.22 | 18.01 | 0.70 1.59 | 1.69 | 1495 | 182 | 0 | 0 | 1677 | 1558 | 15.63 | 17.15 | 24.11 | 0.73 1.69 | 1.82 | 1495 | 173 | 0 | 0 | 1668 | 1539 | 17.86 | 22.56 | 31.01 | 0.76 1.82 | 2.00 | 1503 | 203 | 0 | 0 | 1706 | 1549 | 22.59 | 33.97 | 45.28 | 0.79 2.00 | 2.29 | 1539 | 197 | 0 | 0 | 1736 | 1589 | 29.55 | 52.79 | 67.63 | 0.80 2.29 | 2.88 | 1554 | 181 | 0 | 0 | 1735 | 1630 | 32.68 | 80.83 | 98.92 | 0.80 2.88 | 28.90 | 1572 | 179 | 1 | 0 | 1751 | 1693 | 52.36 | 186.21 | 210.33 | 0.79 --------------------------------------------------------------------------------------------------------- Summary of integration results for the whole dataset --------------------------------------------- Number fully recorded | 24911 Number partially recorded | 3031 Number with overloaded pixels | 5 Number in powder rings | 0 Number processed with summation | 23906 Number processed with profile fitting | 21608 | 18.16 (summation) | 32.18 (profile fitting) | 41.74 | 0.51 --------------------------------------------- ================================================================================ Summary of integration results for experiment 1 Summary of integration results as a function of image number -------------------------------------------------------------------------------- Image | # full | # part | # sum | # prf | | | | | | | | | | (sum) | (prf) | -------------------------------------------------------------------------------- 0 | 287 | 1329 | 1616 | 1100 | 18.51 | 32.45 | 50.08 | 0.67 1 | 532 | 1331 | 1863 | 1330 | 18.52 | 32.34 | 48.37 | 0.67 2 | 767 | 1333 | 2100 | 1549 | 18.60 | 32.59 | 47.70 | 0.67 3 | 1003 | 1335 | 2338 | 1760 | 18.81 | 32.58 | 46.99 | 0.67 4 | 1233 | 1331 | 2564 | 1964 | 18.59 | 32.06 | 45.79 | 0.67 5 | 1481 | 1216 | 2697 | 2117 | 18.42 | 31.95 | 45.18 | 0.67 6 | 1742 | 1056 | 2798 | 2261 | 18.27 | 31.91 | 44.27 | 0.67 7 | 1971 | 850 | 2821 | 2351 | 18.28 | 31.78 | 43.24 | 0.67 8 | 2187 | 655 | 2842 | 2411 | 18.11 | 31.31 | 42.14 | 0.67 9 | 2348 | 528 | 2876 | 2482 | 18.15 | 31.04 | 41.42 | 0.67 10 | 2445 | 447 | 2892 | 2513 | 18.19 | 30.91 | 41.13 | 0.67 11 | 2495 | 390 | 2885 | 2515 | 18.04 | 30.85 | 40.91 | 0.67 12 | 2561 | 350 | 2911 | 2553 | 17.89 | 30.35 | 40.22 | 0.67 13 | 2590 | 317 | 2907 | 2552 | 17.94 | 30.76 | 40.68 | 0.67 14 | 2625 | 289 | 2914 | 2565 | 18.04 | 31.46 | 41.44 | 0.67 15 | 2609 | 274 | 2883 | 2540 | 17.97 | 31.71 | 41.71 | 0.66 16 | 2621 | 262 | 2883 | 2542 | 17.85 | 31.82 | 41.80 | 0.66 17 | 2640 | 250 | 2890 | 2547 | 17.84 | 31.83 | 41.92 | 0.66 18 | 2657 | 237 | 2894 | 2550 | 17.71 | 31.52 | 41.38 | 0.66 19 | 2697 | 219 | 2916 | 2575 | 17.69 | 31.17 | 41.02 | 0.67 20 | 2701 | 208 | 2909 | 2572 | 17.71 | 31.41 | 41.26 | 0.67 21 | 2752 | 196 | 2948 | 2612 | 17.79 | 32.25 | 42.26 | 0.67 22 | 2761 | 186 | 2947 | 2607 | 17.85 | 32.39 | 42.50 | 0.66 23 | 2819 | 182 | 3001 | 2662 | 17.91 | 32.49 | 42.64 | 0.67 24 | 2837 | 182 | 3019 | 2682 | 17.97 | 33.04 | 43.22 | 0.67 25 | 2810 | 176 | 2986 | 2660 | 18.14 | 33.63 | 43.94 | 0.67 26 | 2834 | 169 | 3003 | 2666 | 18.26 | 33.99 | 44.39 | 0.67 27 | 2833 | 165 | 2998 | 2662 | 18.28 | 34.47 | 45.00 | 0.67 28 | 2856 | 162 | 3018 | 2680 | 18.20 | 34.88 | 45.31 | 0.67 29 | 2869 | 160 | 3029 | 2699 | 18.20 | 34.98 | 45.30 | 0.67 30 | 2849 | 161 | 3010 | 2680 | 18.12 | 34.48 | 44.70 | 0.67 31 | 2844 | 160 | 3004 | 2673 | 18.06 | 34.60 | 44.86 | 0.66 32 | 2818 | 162 | 2980 | 2652 | 17.94 | 34.45 | 44.57 | 0.66 33 | 2831 | 163 | 2994 | 2662 | 17.92 | 34.48 | 44.54 | 0.66 34 | 2846 | 159 | 3005 | 2686 | 18.02 | 34.94 | 44.97 | 0.66 35 | 2839 | 159 | 2998 | 2667 | 17.86 | 34.12 | 44.11 | 0.66 36 | 2835 | 158 | 2993 | 2660 | 17.81 | 34.17 | 44.06 | 0.66 37 | 2822 | 156 | 2978 | 2642 | 17.67 | 33.51 | 43.30 | 0.66 38 | 2800 | 155 | 2955 | 2629 | 17.76 | 33.32 | 43.04 | 0.66 39 | 2836 | 154 | 2990 | 2669 | 17.74 | 33.38 | 42.99 | 0.66 40 | 2832 | 152 | 2984 | 2666 | 17.65 | 33.54 | 43.03 | 0.66 41 | 2866 | 154 | 3020 | 2692 | 17.57 | 33.17 | 42.77 | 0.66 42 | 2872 | 155 | 3027 | 2704 | 17.58 | 33.38 | 42.99 | 0.66 43 | 2853 | 154 | 3007 | 2684 | 17.58 | 33.92 | 43.53 | 0.66 44 | 2870 | 155 | 3025 | 2704 | 17.70 | 34.33 | 43.98 | 0.65 45 | 2891 | 155 | 3046 | 2730 | 17.71 | 33.87 | 43.35 | 0.65 46 | 2915 | 147 | 3062 | 2743 | 17.83 | 34.23 | 43.83 | 0.66 47 | 2913 | 148 | 3061 | 2745 | 17.74 | 33.24 | 42.59 | 0.65 48 | 2899 | 146 | 3045 | 2735 | 17.83 | 33.87 | 43.29 | 0.65 49 | 2915 | 145 | 3060 | 2743 | 18.09 | 34.86 | 44.50 | 0.66 50 | 2919 | 145 | 3064 | 2750 | 18.14 | 34.72 | 44.22 | 0.66 51 | 2874 | 144 | 3018 | 2711 | 18.08 | 34.65 | 44.14 | 0.66 52 | 2894 | 146 | 3040 | 2734 | 18.07 | 34.25 | 43.63 | 0.65 53 | 2896 | 147 | 3043 | 2737 | 18.04 | 34.02 | 43.32 | 0.66 54 | 2900 | 145 | 3045 | 2731 | 17.87 | 33.77 | 43.05 | 0.65 55 | 2896 | 146 | 3042 | 2726 | 17.97 | 33.94 | 43.33 | 0.66 56 | 2855 | 147 | 3002 | 2684 | 17.89 | 33.85 | 43.26 | 0.66 57 | 2831 | 146 | 2977 | 2669 | 17.78 | 33.78 | 43.04 | 0.65 58 | 2818 | 144 | 2962 | 2649 | 17.73 | 33.27 | 42.35 | 0.65 59 | 2813 | 146 | 2959 | 2638 | 17.72 | 32.37 | 41.42 | 0.65 60 | 2796 | 150 | 2946 | 2618 | 17.75 | 32.36 | 41.51 | 0.66 61 | 2792 | 155 | 2947 | 2610 | 17.79 | 33.39 | 42.80 | 0.65 62 | 2760 | 155 | 2915 | 2578 | 17.73 | 33.19 | 42.66 | 0.66 63 | 2735 | 156 | 2891 | 2548 | 17.67 | 33.34 | 42.94 | 0.66 64 | 2740 | 158 | 2898 | 2556 | 17.63 | 33.08 | 42.63 | 0.66 65 | 2754 | 160 | 2914 | 2563 | 17.64 | 32.25 | 41.85 | 0.66 66 | 2747 | 162 | 2909 | 2545 | 17.62 | 31.48 | 41.14 | 0.65 67 | 2762 | 166 | 2928 | 2563 | 17.73 | 31.86 | 41.58 | 0.65 68 | 2772 | 168 | 2940 | 2603 | 17.72 | 30.59 | 39.60 | 0.64 69 | 2783 | 165 | 2948 | 2615 | 17.87 | 31.21 | 40.38 | 0.64 70 | 2784 | 161 | 2945 | 2626 | 18.05 | 31.93 | 41.01 | 0.64 71 | 2792 | 163 | 2955 | 2632 | 18.03 | 31.86 | 40.98 | 0.64 72 | 2807 | 169 | 2976 | 2653 | 18.06 | 31.86 | 41.00 | 0.65 73 | 2801 | 172 | 2973 | 2671 | 17.74 | 31.13 | 40.02 | 0.65 74 | 2772 | 180 | 2952 | 2640 | 17.68 | 30.81 | 39.75 | 0.65 75 | 2767 | 185 | 2952 | 2643 | 17.51 | 30.38 | 39.15 | 0.65 76 | 2794 | 194 | 2988 | 2654 | 17.42 | 30.69 | 39.75 | 0.65 77 | 2777 | 199 | 2976 | 2639 | 17.42 | 31.01 | 40.14 | 0.65 78 | 2753 | 209 | 2962 | 2620 | 17.24 | 30.84 | 39.98 | 0.65 79 | 2733 | 226 | 2959 | 2607 | 17.18 | 30.81 | 40.04 | 0.65 80 | 2699 | 235 | 2934 | 2567 | 17.10 | 30.15 | 39.50 | 0.65 81 | 2620 | 244 | 2864 | 2489 | 17.08 | 30.48 | 40.12 | 0.66 82 | 2629 | 253 | 2882 | 2504 | 17.25 | 31.24 | 41.06 | 0.66 83 | 2606 | 269 | 2875 | 2500 | 17.18 | 31.45 | 41.35 | 0.66 84 | 2629 | 282 | 2911 | 2532 | 17.26 | 31.75 | 41.72 | 0.66 85 | 2601 | 302 | 2903 | 2512 | 17.22 | 31.80 | 41.92 | 0.66 86 | 2562 | 332 | 2894 | 2493 | 17.19 | 31.71 | 41.99 | 0.66 87 | 2550 | 365 | 2915 | 2512 | 17.15 | 31.02 | 41.15 | 0.66 88 | 2489 | 413 | 2902 | 2488 | 17.25 | 31.07 | 41.40 | 0.66 89 | 2437 | 467 | 2904 | 2486 | 17.25 | 30.44 | 40.61 | 0.66 90 | 2358 | 548 | 2906 | 2477 | 17.23 | 30.44 | 40.72 | 0.66 91 | 2234 | 668 | 2902 | 2457 | 17.25 | 30.41 | 40.81 | 0.66 92 | 2017 | 837 | 2854 | 2378 | 17.25 | 30.28 | 41.14 | 0.67 93 | 1744 | 1022 | 2766 | 2249 | 17.15 | 29.87 | 41.14 | 0.67 94 | 1510 | 1180 | 2690 | 2124 | 17.23 | 29.72 | 41.72 | 0.67 95 | 1253 | 1295 | 2548 | 1956 | 17.31 | 29.49 | 41.98 | 0.66 96 | 1018 | 1299 | 2317 | 1744 | 17.18 | 29.22 | 41.95 | 0.66 97 | 804 | 1298 | 2102 | 1550 | 17.10 | 29.30 | 42.50 | 0.65 98 | 577 | 1298 | 1875 | 1349 | 16.95 | 28.98 | 42.41 | 0.65 99 | 315 | 1297 | 1612 | 1108 | 17.00 | 30.02 | 45.06 | 0.65 -------------------------------------------------------------------------------- Summary of integration results binned by resolution --------------------------------------------------------------------------------------------------------- d min | d max | # full | # part | # over | # ice | # sum | # prf | | | | | | | | | | | | | (sum) | (prf) | --------------------------------------------------------------------------------------------------------- 1.06 | 1.08 | 32 | 1 | 0 | 0 | 33 | 19 | 4.41 | 1.89 | 3.56 | 0.29 1.08 | 1.10 | 122 | 13 | 0 | 0 | 135 | 91 | 4.79 | 2.21 | 3.75 | 0.36 1.10 | 1.12 | 201 | 17 | 0 | 0 | 218 | 163 | 5.29 | 2.17 | 3.79 | 0.35 1.12 | 1.14 | 326 | 45 | 0 | 0 | 371 | 279 | 5.79 | 2.63 | 4.59 | 0.41 1.14 | 1.17 | 410 | 51 | 0 | 0 | 461 | 387 | 6.35 | 2.91 | 4.86 | 0.42 1.17 | 1.19 | 561 | 59 | 0 | 0 | 620 | 515 | 6.96 | 3.40 | 5.69 | 0.46 1.19 | 1.22 | 797 | 80 | 0 | 0 | 877 | 722 | 7.66 | 3.62 | 6.21 | 0.49 1.22 | 1.26 | 1047 | 108 | 0 | 0 | 1155 | 970 | 8.46 | 4.20 | 7.17 | 0.54 1.26 | 1.29 | 1327 | 173 | 0 | 0 | 1500 | 1251 | 9.18 | 4.41 | 7.49 | 0.54 1.29 | 1.34 | 1441 | 197 | 0 | 0 | 1638 | 1410 | 9.95 | 5.06 | 8.35 | 0.57 1.34 | 1.38 | 1456 | 189 | 0 | 0 | 1645 | 1443 | 10.75 | 5.55 | 9.08 | 0.59 1.38 | 1.44 | 1449 | 192 | 0 | 0 | 1641 | 1432 | 11.71 | 6.97 | 11.29 | 0.65 1.44 | 1.50 | 1475 | 220 | 0 | 0 | 1695 | 1512 | 12.84 | 8.67 | 13.80 | 0.68 1.50 | 1.58 | 1486 | 194 | 0 | 0 | 1680 | 1509 | 13.99 | 11.69 | 17.56 | 0.72 1.58 | 1.68 | 1491 | 200 | 0 | 0 | 1691 | 1517 | 15.61 | 15.12 | 21.66 | 0.73 1.68 | 1.81 | 1490 | 196 | 0 | 0 | 1686 | 1480 | 17.79 | 20.17 | 27.99 | 0.76 1.81 | 2.00 | 1514 | 183 | 0 | 0 | 1697 | 1487 | 22.54 | 30.80 | 40.80 | 0.79 2.00 | 2.28 | 1501 | 235 | 0 | 0 | 1736 | 1495 | 29.61 | 47.66 | 61.68 | 0.80 2.28 | 2.88 | 1537 | 202 | 0 | 0 | 1739 | 1586 | 32.65 | 70.58 | 88.11 | 0.80 2.88 | 25.50 | 1513 | 211 | 0 | 0 | 1724 | 1676 | 52.68 | 171.78 | 193.58 | 0.80 --------------------------------------------------------------------------------------------------------- Summary of integration results for the whole dataset --------------------------------------------- Number fully recorded | 24420 Number partially recorded | 3307 Number with overloaded pixels | 3 Number in powder rings | 0 Number processed with summation | 23942 Number processed with profile fitting | 20944 | 18.11 (summation) | 29.09 (profile fitting) | 38.57 | 0.51 --------------------------------------------- Exporting as MTZ ^^^^^^^^^^^^^^^^ The final step of dials processing is to export the integrated results to mtz format, suitable for input to downstream processing programs such as pointless_ and aimless_. Currently :doc:`dials.export ` only supports one experiment at a time, therefore it is necessary to first split the :samp:`refined_experiments.json` and :samp:`integrated.pickle` into separate files :: dials.split_experiments refined_experiments.json integrated.pickle \ experiments_prefix=refined_experiments reflections_prefix=integrated :: Saving experiment 0 to refined_experiments_0.json Saving reflections for experiment 0 to integrated_0.pickle Saving experiment 1 to refined_experiments_1.json Saving reflections for experiment 1 to integrated_1.pickle Now we are ready to run dials.export on the individual .pickle and .json files output for each experiment. :: dials.export integrated_0.pickle refined_experiments_0.json mtz.hklout=integrated_0.mtz dials.export integrated_1.pickle refined_experiments_1.json mtz.hklout=integrated_1.mtz And this is the output, showing the reflection file statistics. :: Removing 1277 reflections with negative variance Removing 5057 profile reflections with negative variance Removing 1153 incomplete reflections Title: from dials.export Space group symbol from file: P222 Space group number from file: 16 Space group from matrices: P 2 2 2 (No. 16) Point group symbol from file: 222 Number of batches: 100 Number of crystals: 1 Number of Miller indices: 20455 Resolution range: 28.8939 1.06627 History: Crystal 1: Name: XTAL Project: DIALS Id: 1 Unit cell: (54.1146, 58.298, 66.5347, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: FROMDIALS Id: 1 Wavelength: 0.97949 Number of columns: 14 label #valid %valid min max type H 20455 100.00% 0.00 32.00 H: index h,k,l K 20455 100.00% 0.00 51.00 H: index h,k,l L 20455 100.00% 0.00 59.00 H: index h,k,l M_ISYM 20455 100.00% 2.00 8.00 Y: M/ISYM, packed partial/reject flag and symmetry number BATCH 20455 100.00% 3.00 98.00 B: BATCH number IPR 20455 100.00% -9311.98 174317.56 J: intensity SIGIPR 20455 100.00% 24.17 421.85 Q: standard deviation I 20455 100.00% -11542.51 174304.84 J: intensity SIGI 20455 100.00% 29.08 424.15 Q: standard deviation FRACTIONCALC 20455 100.00% 1.00 1.00 R: real XDET 20455 100.00% 11.79 2450.61 R: real YDET 20455 100.00% 9.78 2515.63 R: real ROT 20455 100.00% 0.18 9.62 R: real LP 20455 100.00% 0.01 0.86 R: real Removing 1465 reflections with negative variance Removing 5318 profile reflections with negative variance Removing 1317 incomplete reflections Title: from dials.export Space group symbol from file: P222 Space group number from file: 16 Space group from matrices: P 2 2 2 (No. 16) Point group symbol from file: 222 Number of batches: 100 Number of crystals: 1 Number of Miller indices: 19627 Resolution range: 25.491 1.06429 History: Crystal 1: Name: XTAL Project: DIALS Id: 1 Unit cell: (54.133, 58.3114, 66.5333, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: FROMDIALS Id: 1 Wavelength: 0.97949 Number of columns: 14 label #valid %valid min max type H 19627 100.00% 0.00 37.00 H: index h,k,l K 19627 100.00% 0.00 53.00 H: index h,k,l L 19627 100.00% 0.00 60.00 H: index h,k,l M_ISYM 19627 100.00% 1.00 8.00 Y: M/ISYM, packed partial/reject flag and symmetry number BATCH 19627 100.00% 4.00 97.00 B: BATCH number IPR 19627 100.00% -11344.32 118159.02 J: intensity SIGIPR 19627 100.00% 18.96 348.01 Q: standard deviation I 19627 100.00% -14248.27 116392.28 J: intensity SIGI 19627 100.00% 23.14 347.57 Q: standard deviation FRACTIONCALC 19627 100.00% 1.00 1.00 R: real XDET 19627 100.00% 10.39 2451.64 R: real YDET 19627 100.00% 8.78 2517.64 R: real ROT 19627 100.00% 0.21 9.59 R: real LP 19627 100.00% 0.02 0.87 R: real What to do Next --------------- The following demonstrates how to take the output of dials processing and continue with downstream analysis, first using rebatch_ to ensure that the reflections for each lattice have different batch numbers, and then using pointless_ to sort the data and assign the correct symmetry, followed by scaling with aimless_ and intensity analysis using ctruncate_:: rebatch hklin integrated_0.mtz hklout rebatch_0.mtz > rebatch_0.log << EOF batch add 0 EOF rebatch hklin integrated_1.mtz hklout rebatch_1.mtz > rebatch_1.log << EOF batch add 200 EOF pointless hklin rebatch_0.mtz rebatch_1.mtz hklout sorted.mtz > pointless.log aimless hklin sorted.mtz hklout scaled.mtz > aimless.log << eof anomalous off eof ctruncate -hklin scaled.mtz -hklout truncated.mtz \ -colin '/*/*/[IMEAN,SIGIMEAN]' > ctruncate.log to get merged data for downstream analysis. The output from this will include the merging statistics which will give some idea of the data quality. Often passing in a sensible resolution limit to aimless is also helpful... this should give you something like:: Summary data for Project: DIALS Crystal: XTAL Dataset: FROMDIALS Overall InnerShell OuterShell Low resolution limit 28.89 28.89 1.08 High resolution limit 1.06 5.83 1.06 Rmerge (within I+/I-) 0.034 0.017 0.000 Rmerge (all I+ and I-) 0.037 0.018 0.000 Rmeas (within I+/I-) 0.047 0.024 0.000 Rmeas (all I+ & I-) 0.051 0.024 0.000 Rpim (within I+/I-) 0.033 0.017 0.000 Rpim (all I+ & I-) 0.035 0.016 0.000 Rmerge in top intensity bin 0.022 - - Total number of observations 40064 390 51 Total number unique 31116 285 50 Mean((I)/sd(I)) 7.1 15.8 2.1 Mn(I) half-set correlation CC(1/2) 0.994 0.999 0.000 Completeness 33.1 42.8 1.1 Multiplicity 1.3 1.4 1.0 Anomalous completeness 5.1 9.5 0.0 Anomalous multiplicity 0.2 1.2 1.0 DelAnom correlation between half-sets -0.001 0.000 0.000 Mid-Slope of Anom Normal Probability 0.582 - - Estimates of resolution limits: overall from half-dataset correlation CC(1/2) > 0.50: limit = 1.08A from Mn(I/sd) > 2.00: limit = 1.06A == maximum resolution Estimates of resolution limits in reciprocal lattice directions: Along k axis from half-dataset correlation CC(1/2) > 0.50: limit = 1.12A from Mn(I/sd) > 2.00: limit = 1.06A == maximum resolution Along l axis from half-dataset correlation CC(1/2) > 0.50: limit = 1.14A from Mn(I/sd) > 2.00: limit = 1.12A Anisotropic deltaB (i.e. range of principal components), A^2: 2.00 Average unit cell: 54.12 58.30 66.53 90.00 90.00 90.00 Space group: P 2 2 2 Average mosaicity: 0.00 .. _pointless: http://www.ccp4.ac.uk/html/pointless.html .. _aimless: http://www.ccp4.ac.uk/html/aimless.html .. _ctruncate: http://www.ccp4.ac.uk/html/ctruncate.html .. _rebatch: http://www.ccp4.ac.uk/html/rebatch.html