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iotbx/examples/recalculate_phenix_refine_r_factors.py -text
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iotbx/fullprof/__init__.py -text
iotbx/fullprof/read_pcr.py -text
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iotbx/gui_tools/__init__.py -text
iotbx/gui_tools/cif_conversions.py -text
iotbx/gui_tools/import_data_and_flags.py -text
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iotbx/gui_tools/reflections.py -text
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iotbx/map_tools.py -text
iotbx/merging_statistics.py -text
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iotbx/mtz/tst_extract_from_symmetry_lib.py svneol=native#text/x-python
iotbx/mtz/tst_miller_dict.py -text
iotbx/mtz/tst_unmerged.py -text
iotbx/ncs/__init__.py -text
iotbx/pdb/Hy36.java svneol=native#text/plain
iotbx/pdb/atom_selection.cpp svneol=native#text/plain
iotbx/pdb/atom_selection.py svneol=native#text/x-python
iotbx/pdb/construct_hierarchy.cpp svneol=native#text/plain
iotbx/pdb/download.py -text
iotbx/pdb/extract_rfactors_resolutions_sigma.py -text
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iotbx/pdb/hierarchy.py svneol=native#text/x-python
iotbx/pdb/hierarchy_atom_bpl.cpp svneol=native#text/plain
iotbx/pdb/hierarchy_atoms.cpp svneol=native#text/plain
iotbx/pdb/hierarchy_atoms.h svneol=native#text/plain
iotbx/pdb/hierarchy_atoms_bpl.cpp svneol=native#text/plain
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iotbx/pdb/hierarchy_select.cpp svneol=native#text/plain
iotbx/pdb/hierarchy_write.cpp svneol=native#text/plain
iotbx/pdb/hybrid_36_cpp.cpp svneol=native#text/plain
iotbx/pdb/hybrid_36_cpp.h svneol=native#text/plain
iotbx/pdb/input.cpp svneol=native#text/plain
iotbx/pdb/input_write.cpp svneol=native#text/plain
iotbx/pdb/misc_records_output.py -text
iotbx/pdb/mmcif.py -text
iotbx/pdb/modified_aa_names.h -text
iotbx/pdb/modified_rna_dna_names.h -text
iotbx/pdb/namespace.h svneol=native#text/plain
iotbx/pdb/overall_counts.cpp svneol=native#text/plain
iotbx/pdb/pdbe.py -text
iotbx/pdb/rcsb.py -text
iotbx/pdb/records.py svneol=native#text/x-python
iotbx/pdb/remediation/__init__.py svneol=native#text/x-python
iotbx/pdb/remediation/remediation.dict -text
iotbx/pdb/remediation/remediator.py svneol=native#text/x-python
iotbx/pdb/rna_dna_atom_names.h -text
iotbx/pdb/rna_dna_atom_names_bpl.cpp -text
iotbx/pdb/rna_dna_detection.py svneol=native#text/x-python
iotbx/pdb/secondary_structure.py -text
iotbx/pdb/tst_atom_selection.py svneol=native#text/x-python
iotbx/pdb/tst_atom_selection_string.py -text
iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py -text
iotbx/pdb/tst_hierarchy.py svneol=native#text/x-python
iotbx/pdb/tst_hierarchy_atom_sort.py -text
iotbx/pdb/tst_mmcif.py -text
iotbx/pdb/tst_mmcif_hierarchy.py -text
iotbx/pdb/tst_read_mtrix_records_from_cif.py -text
iotbx/pdb/tst_rna_dna_atom_names.py -text
iotbx/pdb/tst_secondary_structure.py -text
iotbx/pdb/tst_secondary_structure_2.py -text
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iotbx/poscar.py svneol=native#text/x-python
iotbx/ranges.py -text
iotbx/reflection_file_editor.py -text
iotbx/regression/ncs/__init__.py -text
iotbx/regression/ncs/tst_ncs_groups_preprocessing.py -text
iotbx/regression/ncs/tst_ncs_input.py -text
iotbx/regression/ncs/tst_ncs_user_selections.py -text
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mmtbx/command_line/model_vs_data.py -text
mmtbx/command_line/model_vs_map.py -text
mmtbx/command_line/model_vs_sequence.py -text
mmtbx/command_line/models_as_chains.py -text
mmtbx/command_line/molprobity.py svneol=native#text/x-python
mmtbx/command_line/mon_lib_cif_triage.py svneol=native#text/x-python
mmtbx/command_line/mp_geo.py -text
mmtbx/command_line/mtz2map.py -text
mmtbx/command_line/nonbonded_overlaps.py -text
mmtbx/command_line/nqh_minimize.py -text
mmtbx/command_line/omegalyze.py -text
mmtbx/command_line/partial_omit_map.py svneol=native#text/x-python
mmtbx/command_line/pdb_atom_selection.py svneol=native#text/x-python
mmtbx/command_line/pdb_view_ad_hoc.py svneol=native#text/x-python
mmtbx/command_line/pdbtools.py -text
mmtbx/command_line/perigee.py -text
mmtbx/command_line/plan_sad_experiment.py -text
mmtbx/command_line/polder.py -text
mmtbx/command_line/prepare_pdb_deposition.py -text
mmtbx/command_line/prune_model.py -text
mmtbx/command_line/r_factor_statistics.py -text
mmtbx/command_line/ramalyze.py -text
mmtbx/command_line/rank_scale_map.py -text
mmtbx/command_line/real_space_correlation.py -text
mmtbx/command_line/reciprocal_space_arrays.py -text
mmtbx/command_line/refine_anomalous_substructure.py -text
mmtbx/command_line/rigid_bond_test.py -text
mmtbx/command_line/ringer.py -text
mmtbx/command_line/rna_validate.py svneol=native#text/x-python
mmtbx/command_line/rotalyze.py -text
mmtbx/command_line/search_pdb_symmetry.py -text
mmtbx/command_line/secondary_structure_restraints.py -text
mmtbx/command_line/select_best_starting_model.py -text
mmtbx/command_line/show_r_factors_by_shell.py -text
mmtbx/command_line/show_suspicious_residues.py -text
mmtbx/command_line/simulate_low_res_data.py -text
mmtbx/command_line/sisa.py -text
mmtbx/command_line/sort_hetatms.py -text
mmtbx/command_line/ssm_rmsd_for_chains.py -text
mmtbx/command_line/strip_model.py svneol=native#text/x-python
mmtbx/command_line/superpose.py -text
mmtbx/command_line/table_one.py svneol=native#text/x-python
mmtbx/command_line/tls.py -text
mmtbx/command_line/tls_analysis.py -text
mmtbx/command_line/tls_as_xyz.py -text
mmtbx/command_line/validate_ions.py -text
mmtbx/command_line/validate_ligands.py -text
mmtbx/command_line/validate_waters.py -text
mmtbx/command_line/validation_summary.py -text
mmtbx/command_line/verify_mon_lib_data.py -text
mmtbx/command_line/water_screen.py -text
mmtbx/command_line/xmanip.py -text
mmtbx/conformation_dependent_library/__init__.py -text
mmtbx/conformation_dependent_library/altloc_weighting.py -text
mmtbx/conformation_dependent_library/bond_angle_registry.py -text
mmtbx/conformation_dependent_library/cdl_database.py -text
mmtbx/conformation_dependent_library/cdl_setup.py -text
mmtbx/conformation_dependent_library/cdl_utils.py -text
mmtbx/conformation_dependent_library/check_cdl_database.py -text
mmtbx/conformation_dependent_library/histidines.py -text
mmtbx/conformation_dependent_library/hpdl_database.py -text
mmtbx/conformation_dependent_library/hydrogen_bonding.py -text
mmtbx/conformation_dependent_library/investigate_rotamer_space.py -text
mmtbx/conformation_dependent_library/multi_residue_class.py -text
mmtbx/conformation_dependent_library/omega.py -text
mmtbx/conformation_dependent_library/omega_database.py -text
mmtbx/conformation_dependent_library/pH_dependent_restraints.py -text
mmtbx/conformation_dependent_library/rdl_database.py -text
mmtbx/conformation_dependent_library/rotamers.py -text
mmtbx/conformation_dependent_library/test_cdl.py -text
mmtbx/conformation_dependent_library/test_cdl_esd.py -text
mmtbx/conformation_dependent_library/test_hpdl.py -text
mmtbx/conformation_dependent_library/test_omega_cdl.py -text
mmtbx/conformation_dependent_library/test_rdl.py -text
mmtbx/conformation_dependent_library/utils.py -text
mmtbx/den/SConscript -text
mmtbx/den/__init__.py svneol=native#text/x-python
mmtbx/den/boost_python/den_ext.cpp svneol=native#text/plain
mmtbx/den/den.h svneol=native#text/plain
mmtbx/den/plot_weights.py -text
mmtbx/den/refinement.py svneol=native#text/x-python
mmtbx/density_modification/__init__.py -text
mmtbx/density_modification/tst_density_modification.py -text
mmtbx/disorder/__init__.py -text
mmtbx/disorder/analyze_model.py -text
mmtbx/disorder/backbone.py -text
mmtbx/disorder/tst.py -text
mmtbx/disorder/tst_analyze_model.py -text
mmtbx/disorder/tst_backbone.py -text
mmtbx/dynamics/constants.py svneol=native#text/x-python
mmtbx/dynamics/ensemble_cd.py svneol=native#text/x-python
mmtbx/dynamics/tst_sa.py -text
mmtbx/email_ralf_042910.txt -text
mmtbx/examples/simple_command_line_cc.py -text
mmtbx/f_model/__init__.py -text
mmtbx/f_model/f_model_info.py -text
mmtbx/f_model_info.py -text
mmtbx/find_peaks.py -text
mmtbx/geometry/SConscript -text
mmtbx/geometry/__init__.py -text
mmtbx/geometry/altloc.py -text
mmtbx/geometry/asa.hpp -text
mmtbx/geometry/asa.hxx -text
mmtbx/geometry/asa.py -text
mmtbx/geometry/boost_python/asa_ext.cpp -text
mmtbx/geometry/boost_python/clash_ext.cpp -text
mmtbx/geometry/boost_python/containment.hpp -text
mmtbx/geometry/boost_python/indexing.hpp -text
mmtbx/geometry/boost_python/indexing_ext.cpp -text
mmtbx/geometry/boost_python/primitive_ext.cpp -text
mmtbx/geometry/boost_python/shared_types_ext.cpp -text
mmtbx/geometry/boost_python/sphere_surface_sampling_ext.cpp -text
mmtbx/geometry/calculator.hpp -text
mmtbx/geometry/clash.hpp -text
mmtbx/geometry/clash.hxx -text
mmtbx/geometry/clash.py -text
mmtbx/geometry/containment.hpp -text
mmtbx/geometry/containment.hxx -text
mmtbx/geometry/flattening.hpp -text
mmtbx/geometry/indexing.hpp -text
mmtbx/geometry/indexing.hxx -text
mmtbx/geometry/indexing.py -text
mmtbx/geometry/overlap.hpp -text
mmtbx/geometry/overlap.hxx -text
mmtbx/geometry/primitive.hpp -text
mmtbx/geometry/primitive.hxx -text
mmtbx/geometry/shared_types.py -text
mmtbx/geometry/sphere_surface_sampling.hpp -text
mmtbx/geometry/sphere_surface_sampling.hxx -text
mmtbx/geometry/sphere_surface_sampling.py -text
mmtbx/geometry/tests/1ahq_trunc.pdb -text
mmtbx/geometry/tests/tst_altloc.py -text
mmtbx/geometry/tests/tst_asa.py -text
mmtbx/geometry/tests/tst_clash.py -text
mmtbx/geometry/tests/tst_indexing.py -text
mmtbx/geometry/tests/tst_shared_types.py -text
mmtbx/geometry/tests/tst_sphere_surface_sampling.py -text
mmtbx/geometry/tests/tst_topology.py -text
mmtbx/geometry/topology.py -text
mmtbx/geometry_restraints/SConscript -text
mmtbx/geometry_restraints/__init__.py -text
mmtbx/geometry_restraints/afitt.py -text
mmtbx/geometry_restraints/boost_python/ramachandran_ext.cpp -text
mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.cpp svneol=native#text/plain
mmtbx/geometry_restraints/c_beta.py svneol=native#text/x-python
mmtbx/geometry_restraints/external.py -text
mmtbx/geometry_restraints/ramachandran.h -text
mmtbx/geometry_restraints/ramachandran.py -text
mmtbx/geometry_restraints/reference.py svneol=native#text/x-python
mmtbx/geometry_restraints/reference_coordinate.h svneol=native#text/plain
mmtbx/geometry_restraints/torsion_restraints/__init__.py svneol=native#text/x-python
mmtbx/geometry_restraints/torsion_restraints/reference_model.py svneol=native#text/x-python
mmtbx/geometry_restraints/torsion_restraints/rotamer_search.py -text
mmtbx/geometry_restraints/torsion_restraints/torsion_ncs.py svneol=native#text/x-python
mmtbx/geometry_restraints/torsion_restraints/tst_reference_model.py svneol=native#text/x-python
mmtbx/geometry_restraints/torsion_restraints/tst_torsion_ncs.py -text
mmtbx/geometry_restraints/torsion_restraints/utils.py svneol=native#text/x-python
mmtbx/geometry_restraints/tst_c_beta_restraints.py -text
mmtbx/geometry_restraints/tst_manager.py -text
mmtbx/geometry_restraints/tst_ramachandran.py -text
mmtbx/geometry_restraints/tst_reference_coordinate.py svneol=native#text/x-python
mmtbx/geometry_restraints/tst_reference_coordinate2.py -text
mmtbx/grow_density.py -text
mmtbx/hydrogens/connectivity.py -text
mmtbx/hydrogens/find.py -text
mmtbx/hydrogens/parameterization.py -text
mmtbx/hydrogens/riding.py -text
mmtbx/hydrogens/tst.py -text
mmtbx/hydrogens/tst_connectivity.py -text
mmtbx/hydrogens/tst_parameterization_1.py -text
mmtbx/hydrogens/tst_parameterization_2.py -text
mmtbx/hydrogens/tst_parameterization_3.py -text
mmtbx/hydrogens/tst_parameterization_4.py -text
mmtbx/hydrogens/tst_parameterization_5.py -text
mmtbx/hydrogens/tst_parameterization_6.py -text
mmtbx/hydrogens/tst_riding_fd_1.py -text
mmtbx/hydrogens/tst_riding_fd_2.py -text
mmtbx/hydrogens/tst_riding_fd_3.py -text
mmtbx/hydrogens/tst_riding_fd_4.py -text
mmtbx/hydrogens/tst_riding_fd_5.py -text
mmtbx/hydrogens/tst_riding_minimize.py -text
mmtbx/ias/__init__.py -text
mmtbx/ias/tst_ias.py -text
mmtbx/idealized_aa_residues/__init__.py -text
mmtbx/idealized_aa_residues/data/ala.pdb -text
mmtbx/idealized_aa_residues/data/arg-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/arg.pdb -text
mmtbx/idealized_aa_residues/data/asn-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/asn.pdb -text
mmtbx/idealized_aa_residues/data/asp-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/asp.pdb -text
mmtbx/idealized_aa_residues/data/cys-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/cys.pdb -text
mmtbx/idealized_aa_residues/data/gln-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/gln.pdb -text
mmtbx/idealized_aa_residues/data/glu-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/glu.pdb -text
mmtbx/idealized_aa_residues/data/gly.pdb -text
mmtbx/idealized_aa_residues/data/his-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/his.pdb -text
mmtbx/idealized_aa_residues/data/ile-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/ile.pdb -text
mmtbx/idealized_aa_residues/data/leu-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/leu.pdb -text
mmtbx/idealized_aa_residues/data/lys-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/lys.pdb -text
mmtbx/idealized_aa_residues/data/met-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/met.pdb -text
mmtbx/idealized_aa_residues/data/mse-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/mse.pdb -text
mmtbx/idealized_aa_residues/data/phe-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/phe.pdb -text
mmtbx/idealized_aa_residues/data/pro-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/pro.pdb -text
mmtbx/idealized_aa_residues/data/ser-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/ser.pdb -text
mmtbx/idealized_aa_residues/data/summary-coarse-step10.log -text
mmtbx/idealized_aa_residues/data/thr-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/thr.pdb -text
mmtbx/idealized_aa_residues/data/trp-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/trp.pdb -text
mmtbx/idealized_aa_residues/data/tyr-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/tyr.pdb -text
mmtbx/idealized_aa_residues/data/val-coarse_step10.pickle -text
mmtbx/idealized_aa_residues/data/val.pdb -text
mmtbx/idealized_aa_residues/rotamer_manager.py -text
mmtbx/idealized_aa_residues/sample_rotamers.py -text
mmtbx/idealized_aa_residues/tst.py -text
mmtbx/ions/__init__.py -text
mmtbx/ions/build.py -text
mmtbx/ions/environment.py -text
mmtbx/ions/geometry.py -text
mmtbx/ions/halides.py svneol=native#text/x-python
mmtbx/ions/identify.py svneol=native#text/x-python
mmtbx/ions/ion_parameters.cif -text
mmtbx/ions/svm/__init__.py -text
mmtbx/ions/svm/dump_sites.py -text
mmtbx/ions/svm/tst_classifier.py -text
mmtbx/ions/svm/tst_dump_sites.py -text
mmtbx/ions/svm/tst_vector.py -text
mmtbx/ions/svm/utils.py -text
mmtbx/ions/tst_environment.py -text
mmtbx/ions/tst_geometries.py -text
mmtbx/ions/tst_parameters.py svneol=native#text/x-python
mmtbx/ions/tst_pick_approx_zn.py -text
mmtbx/ions/tst_pick_ca.py -text
mmtbx/ions/tst_pick_ca_svm.py svneol=native#text/x-python
mmtbx/ions/tst_pick_k.py -text
mmtbx/ions/tst_pick_mg.py -text
mmtbx/ions/tst_pickle.py -text
mmtbx/ions/tst_symmetry_axis.py svneol=native#text/x-python
mmtbx/ions/tst_utils.py svneol=native#text/x-python
mmtbx/ions/tst_validate_ca.py -text
mmtbx/ions/tst_validate_mg.py -text
mmtbx/ions/tst_validate_zn.py -text
mmtbx/ions/utils.py svneol=native#text/x-python
mmtbx/kinemage/__init__.py -text
mmtbx/kinemage/validation.py -text
mmtbx/lattice.py -text
mmtbx/libtbx_refresh.py svneol=native#text/x-python
mmtbx/ligands/__init__.py -text
mmtbx/ligands/crystallization_screens.cif -text
mmtbx/ligands/tst_xtal_screens.py -text
mmtbx/ligands/xtal_screens.py -text
mmtbx/map_tools.py -text
mmtbx/maps/__init__.py -text
mmtbx/maps/composite_omit_map.py -text
mmtbx/maps/correlation.py -text
mmtbx/maps/fem.py -text
mmtbx/maps/fobs_minus_fobs_map.py -text
mmtbx/maps/kick.py -text
mmtbx/maps/superpose.py -text
mmtbx/maps/tst_composite_omit_map.py -text
mmtbx/maps/tst_composite_omit_map_2.py -text
mmtbx/maps/tst_composite_omit_map_3.py -text
mmtbx/maps/tst_utils.py -text
mmtbx/maps/utils.py -text
mmtbx/masks/__init__.py -text
mmtbx/masks/atom_mask.cpp svneol=native#text/plain
mmtbx/masks/atom_mask.h svneol=native#text/plain
mmtbx/masks/grid_symop.h svneol=native#text/plain
mmtbx/masks/tst_asu_mask.py svneol=native#text/x-python
mmtbx/masks/tst_mask.cpp svneol=native#text/plain
mmtbx/masks/util.h svneol=native#text/plain
mmtbx/model_vs_data.py -text
mmtbx/monomer_library/bondlength_defaults.py -text
mmtbx/monomer_library/cif_triage.py svneol=native#text/x-python
mmtbx/monomer_library/conformation_dependent_restraints.py svneol=native#text/x-python
mmtbx/monomer_library/conv_v2_v3.py svneol=native#text/x-python
mmtbx/monomer_library/correct_hydrogen_geometries.py -text
mmtbx/monomer_library/glyco_chiral_values.py -text
mmtbx/monomer_library/glyco_utils.py -text
mmtbx/monomer_library/idealized_aa.py -text
mmtbx/monomer_library/linking_mixins.py -text
mmtbx/monomer_library/linking_setup.py -text
mmtbx/monomer_library/linking_utils.py -text
mmtbx/monomer_library/rna_sugar_pucker_analysis.py svneol=native#text/x-python
mmtbx/monomer_library/rotamer_utils.py svneol=native#text/x-python
mmtbx/monomer_library/tst_chg.py -text
mmtbx/monomer_library/tst_cif_triage.py svneol=native#text/x-python
mmtbx/monomer_library/tst_conformation_dependent_restraints.py svneol=native#text/x-python
mmtbx/monomer_library/tst_correct_hydrogens.py -text
mmtbx/monomer_library/tst_geo_reduce_for_tardy.py svneol=native#text/x-python
mmtbx/monomer_library/tst_idealized_aa.py -text
mmtbx/monomer_library/tst_linking.py -text
mmtbx/monomer_library/tst_neutron_distance.py -text
mmtbx/monomer_library/tst_pdb_interpretation_ncs_processing.py -text
mmtbx/monomer_library/tst_protein_interpretation.py -text
mmtbx/monomer_library/tst_rna_dna_interpretation.py -text
mmtbx/monomer_library/tst_rna_sugar_pucker_analysis.py svneol=native#text/x-python
mmtbx/monomer_library/tst_rotamer_utils.py svneol=native#text/x-python
mmtbx/msa.py -text
mmtbx/ncs/ligands.py -text
mmtbx/ncs/ncs_search.py -text
mmtbx/ncs/ncs_utils.py -text
mmtbx/ncs/tncs.h -text
mmtbx/ncs/tncs.py -text
mmtbx/ncs/tncs_ext.cpp -text
mmtbx/pdb_distances.py -text
mmtbx/pdb_symmetry.py -text
mmtbx/pdbtools.py -text
mmtbx/polygon/__init__.py -text
mmtbx/polygon/output.py -text
mmtbx/polygon/tst.py -text
mmtbx/polygon/tst_gui.py -text
mmtbx/proq2.py -text
mmtbx/real_space_correlation.py -text
mmtbx/refinement/ensemble_refinement/__init__.py svneol=native#text/x-python
mmtbx/refinement/ensemble_refinement/ensemble_probability.py -text
mmtbx/refinement/ensemble_refinement/ensemble_utils.py svneol=native#text/x-python
mmtbx/refinement/ensemble_refinement/maps.params -text
mmtbx/refinement/ensemble_refinement/scripts/ens_pdb.py -text
mmtbx/refinement/ensemble_refinement/scripts/ens_tools.py -text
mmtbx/refinement/flip_peptide_side_chain.py -text
mmtbx/refinement/geometry_minimization.py -text
mmtbx/refinement/inspect_tardy_trajectory.py svneol=native#text/x-python
mmtbx/refinement/minimization_ncs_constraints.py -text
mmtbx/refinement/occupancies.py -text
mmtbx/refinement/orca.py svneol=native#text/x-python
mmtbx/refinement/real_space/__init__.py -text
mmtbx/refinement/real_space/adp.py -text
mmtbx/refinement/real_space/explode_and_refine.py -text
mmtbx/refinement/real_space/fit_residue.py -text
mmtbx/refinement/real_space/fit_residues.py -text
mmtbx/refinement/real_space/fit_small_molecule.py -text
mmtbx/refinement/real_space/fit_water.py -text
mmtbx/refinement/real_space/flipbase.py -text
mmtbx/refinement/real_space/individual_sites.py -text
mmtbx/refinement/real_space/rigid_body.py -text
mmtbx/refinement/real_space/tst_aa_residue_axes_and_clusters.py -text
mmtbx/refinement/real_space/tst_fit_residue_0.py -text
mmtbx/refinement/real_space/tst_fit_residue_1.py -text
mmtbx/refinement/real_space/tst_fit_residue_2.py -text
mmtbx/refinement/real_space/tst_fit_residue_3.py -text
mmtbx/refinement/real_space/tst_fit_residue_4.py -text
mmtbx/refinement/real_space/tst_fit_residue_5.py -text
mmtbx/refinement/real_space/tst_fit_residue_6.py -text
mmtbx/refinement/real_space/tst_fit_residue_7.py -text
mmtbx/refinement/real_space/tst_fit_residues_1.py -text
mmtbx/refinement/real_space/tst_fit_residues_2.py -text
mmtbx/refinement/real_space/tst_fit_residues_3.py -text
mmtbx/refinement/real_space/tst_fit_residues_4.py -text
mmtbx/refinement/real_space/tst_fit_water.py -text
mmtbx/refinement/real_space/tst_flipbase.py -text
mmtbx/refinement/real_space/tst_individual_sites_1.py -text
mmtbx/refinement/real_space/tst_individual_sites_2.py -text
mmtbx/refinement/real_space/tst_individual_sites_3.py -text
mmtbx/refinement/real_space/tst_monitor.py -text
mmtbx/refinement/real_space/tst_rigid_body.py -text
mmtbx/refinement/real_space/tst_weight.py -text
mmtbx/refinement/real_space/utils.py -text
mmtbx/refinement/real_space/weight.py -text
mmtbx/refinement/refinement_flags.py -text
mmtbx/refinement/select_best_starting_model.py -text
mmtbx/refinement/tardy.py svneol=native#text/x-python
mmtbx/refinement/targets.py -text
mmtbx/refinement/tst_fit_rotamers.py svneol=native#text/x-python
mmtbx/refinement/tst_group.py -text
mmtbx/refinement/tst_group_2.py -text
mmtbx/refinement/tst_misc.py -text
mmtbx/refinement/tst_occupancy_selections.py svneol=native#text/x-python
mmtbx/refinement/tst_real_space_simple.py -text
mmtbx/refinement/tst_refinement_flags.py -text
mmtbx/refinement/tst_rigid_body_groups_from_pdb_chains.py -text
mmtbx/refinement/tst_select_best_starting_model.py -text
mmtbx/refinement/tst_tardy_comprehensive.py svneol=native#text/x-python
mmtbx/refinement/tst_tardy_eval.py svneol=native#text/x-python
mmtbx/refinement/tst_tardy_pdb.py svneol=native#text/x-python
mmtbx/refinement/utils.py -text
mmtbx/refinement/weights_params.py -text
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rstbx/command_line/__init__.py -text
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rstbx/command_line/index.py -text
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rstbx/command_line/viewer.py -text
rstbx/detectors/__init__.py -text
rstbx/detectors/silicon.py -text
rstbx/dials_core/__init__.py -text
rstbx/dials_core/integration_core.py -text
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rstbx/diffraction/ewald_sphere.cpp -text
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rstbx/diffraction/fastbragg/SConscript -text
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rstbx/diffraction/fastbragg/fastbragg.h -text
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rstbx/diffraction/fastbragg/tst_bragg_minimal.py -text
rstbx/diffraction/fastbragg/tst_utils_clustering.py -text
rstbx/diffraction/partial_spot_position_partial_H.cpp -text
rstbx/diffraction/partial_spot_position_partial_H.h -text
rstbx/diffraction/reflection_range.h -text
rstbx/diffraction/tst_ewald_sphere.py -text
rstbx/diffraction/tst_partial_derivatives.py -text
rstbx/diffraction/tst_predict.py -text
rstbx/dps_core/__init__.py -text
rstbx/dps_core/basis_choice.py -text
rstbx/dps_core/cell_assessment.py -text
rstbx/dps_core/constrainment.py -text
rstbx/dps_core/direction.cpp -text
rstbx/dps_core/direction.h -text
rstbx/dps_core/directional_fft.cpp -text
rstbx/dps_core/directional_fft.h -text
rstbx/dps_core/dps_core.cpp -text
rstbx/dps_core/dps_core.h -text
rstbx/dps_core/lepage.py -text
rstbx/dps_core/sampling.py -text
rstbx/dps_core/spotclass.h -text
rstbx/dps_core/tst_iotbx_converter.py -text
rstbx/dps_core/zuoreduction.py -text
rstbx/ext.cpp -text
rstbx/import_scitbx_af.hpp svneol=native#text/plain
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rstbx/indexing/do_index.py -text
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rstbx/indexing/si_brief.dat -text
rstbx/indexing/si_synthetic.dat -text
rstbx/indexing/tst_auto_monoscan.py -text
rstbx/indexing/tst_dataset1.py -text
rstbx/indexing_api/SConscript -text
rstbx/indexing_api/__init__.py -text
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rstbx/indexing_api/force_cell.py -text
rstbx/indexing_api/indexing_api.cpp -text
rstbx/indexing_api/indexing_api.h -text
rstbx/indexing_api/lattice.py -text
rstbx/indexing_api/nearest_neighbor.py -text
rstbx/indexing_api/outlier_detection.py -text
rstbx/indexing_api/outlier_procedure.py -text
rstbx/indexing_api/sampling.py -text
rstbx/indexing_api/test_dps.py -text
rstbx/indexing_api/tools.py -text
rstbx/libtbx_config -text
rstbx/new_horizons/__init__.py -text
rstbx/new_horizons/index.py -text
rstbx/new_horizons/pixel_spread.py -text
rstbx/new_horizons/speckfinder.py -text
rstbx/new_horizons/spot_shape.py -text
rstbx/new_horizons/stats_index.py -text
rstbx/outlier_spots/__init__.py -text
rstbx/outlier_spots/fit_distribution.py -text
rstbx/phil/__init__.py -text
rstbx/phil/phil_preferences.py -text
rstbx/phil/preferences.py -text
rstbx/phil/scope.py -text
rstbx/run_tests.py -text
rstbx/simage/SConscript -text
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rstbx/simage/explore_completeness.py svneol=native#text/x-python
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rstbx/simage/refine_uc_cr.py svneol=native#text/x-python
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rstbx/simage/tst.py svneol=native#text/x-python
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rstbx/simulation/SConscript -text
rstbx/simulation/__init__.py -text
rstbx/simulation/constants.py -text
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rstbx/simulation/sim_pdf.py -text
rstbx/simulation/sim_utils.py -text
rstbx/simulation/sim_xfel1.h -text
rstbx/simulation/tst_xfel1_simple.py -text
rstbx/slip_viewer/example_frame_plugin_hidden.py -text
rstbx/slip_viewer/slip_viewer_image_factory.py -text
rstbx/symmetry/__init__.py -text
rstbx/symmetry/constraints/SConscript -text
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rstbx/symmetry/constraints/parameter_reduction.py -text
rstbx/symmetry/sgtbx_adaptor.py -text
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rstbx/utils.py -text
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scitbx/array_family/boost_python/passing_flex_by_reference.h -text
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scitbx/array_family/boost_python/tst_flex_argument_passing.py -text
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scitbx/array_family/initialiser.h -text
scitbx/array_family/owning_ref.h -text
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scitbx/boost_python/pair_as_tuple.hpp -text
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scitbx/command_line/show_exp_times.py svneol=native#text/x-python
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scitbx/cross_entropy.py -text
scitbx/cubicle_neighbors.hpp svneol=native#text/plain
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scitbx/direct_search_simulated_annealing.py -text
scitbx/error/SConscript -text
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scitbx/examples/bevington/SConscript -text
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scitbx/examples/principal_axes_of_inertia.py svneol=native#text/x-python
scitbx/examples/rigid_body_refinement_core.py svneol=native#text/x-python
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scitbx/fftpack/boost_python/threads.d -text
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scitbx/glmtbx/boost_python/ext.cc -text
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scitbx/graph/__init__.py -text
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scitbx/graph/tst_rigidity.py -text
scitbx/graph/tst_tardy_tree.py svneol=native#text/x-python
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scitbx/graphics_utils/SConscript -text
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scitbx/lbfgs/dev/run.py -text
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scitbx/linalg/__init__.py -text
scitbx/linalg/boost_python/SConscript -text
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scitbx/lstbx/memory.nb -text
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scitbx/math/2d_zernike_moments.h -text
scitbx/math/angle_derivative.h -text
scitbx/math/approx_equal.h -text
scitbx/math/besselk.py -text
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scitbx/math/clustering.py -text
scitbx/math/continued_fraction.h -text
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scitbx/math/cubic_equation.h -text
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scitbx/math/fliege_mayer_400.py -text
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scitbx/math/sphere_sphere_intersection.py svneol=native#text/x-python
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scitbx/math/tests/SConscript -text
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scitbx/math/tests/tst_weighted_correlation.py svneol=native#text/x-python
scitbx/math/tetrahedron-volume.nb -text
scitbx/math/traits.h -text
scitbx/math/tst_2d_zernike.py -text
scitbx/math/tst_bessel_zeros.py -text
scitbx/math/tst_multivariate_moments.py -text
scitbx/math/tst_so3_lie_algebra.py -text
scitbx/math/tst_undirected_graph.py -text
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scitbx/math/weighted_covariance.h -text
scitbx/math/zernike.h -text
scitbx/math/zernike_align_fft.py -text
scitbx/math/zernike_moments.h -text
scitbx/matrix/bidiagonalisation_flops.nb -text
scitbx/matrix/delta_tensors.h -text
scitbx/matrix/givens.h -text
scitbx/matrix/householder.h -text
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scitbx/matrix/norms.h -text
scitbx/matrix/rotation_formula.tex -text
scitbx/matrix/row_echelon.py svneol=native#text/x-python
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scitbx/matrix/svd.h -text
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scitbx/matrix/tensor_transform_as_linear_map.nb -text
scitbx/matrix/tests.h -text
scitbx/matrix/tests/SConscript -text
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scitbx/matrix/tests/tst_svd.nb -text
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scitbx/matrix/triangular_systems.h -text
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scitbx/misc/positive_getitem_index.h svneol=native#text/plain
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scitbx/regular_grid_on_unit_sphere.py -text
scitbx/rigid_body/SConscript -text
scitbx/rigid_body/__init__.py svneol=native#text/x-python
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scitbx/rigid_body/essence/featherstone.py svneol=native#text/x-python
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scitbx/rigid_body/essence/make_bundles.py svneol=native#text/x-python
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scitbx/rigid_body/ext.cpp svneol=native#text/plain
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scitbx/rigid_body/proto/__init__.py svneol=native#text/x-python
scitbx/rigid_body/proto/featherstone.py svneol=native#text/x-python
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xfel/cxi/cspad_ana/mod_radial_average.py -text
xfel/cxi/cspad_ana/mod_spectrum_filter.py -text
xfel/cxi/cspad_ana/mod_spectrum_filter_remote_only.py -text
xfel/cxi/cspad_ana/mod_spectrum_filter_v2.py -text
xfel/cxi/cspad_ana/pixel_histograms.py -text
xfel/cxi/cspad_ana/pyana_hitfind.cfg -text
xfel/cxi/cspad_ana/rayonix_tbx.py -text
xfel/cxi/cspad_ana/xes_faster_histograms.py -text
xfel/cxi/cspad_ana/xes_histograms.py -text
xfel/cxi/data_utils.py -text
xfel/cxi/display_powder_arcs.py -text
xfel/cxi/gfx/__init__.py -text
xfel/cxi/gfx/trials_plot.py -text
xfel/cxi/gfx/wx_detectors.py -text
xfel/cxi/integrate_image_api.py -text
xfel/cxi/merging_utils.py -text
xfel/cxi/postrefinement_factory.py -text
xfel/cxi/postrefinement_hybrid_rs.py -text
xfel/cxi/postrefinement_legacy_rs.py -text
xfel/cxi/postrefinement_updated_rs.py -text
xfel/cxi/spectra_filter.py -text
xfel/cxi/strong_zulu.py -text
xfel/cxi/trumpet_plot.py -text
xfel/cxi/util.py -text
xfel/graph_proc/__init__.py -text
xfel/graph_proc/components.py -text
xfel/graph_proc/graph.py -text
xfel/graph_proc/multiproc_temp_parame_opt.py -text
xfel/graph_proc/parameter_optimizer.py -text
xfel/libtbx_config -text
xfel/libtbx_refresh.py -text
xfel/merging/__init__.py -text
xfel/merging/absorption.py -text
xfel/merging/phil_validation.py -text
xfel/metrology/__init__.py -text
xfel/metrology/legacy_scale/__init__.py -text
xfel/metrology/legacy_scale/a_g_conversion.h -text
xfel/metrology/legacy_scale/bandpass_gaussian.cpp -text
xfel/metrology/legacy_scale/bandpass_gaussian.h -text
xfel/metrology/legacy_scale/ext.cpp -text
xfel/metrology/legacy_scale/parameters.h -text
xfel/metrology/legacy_scale/quadrants.h -text
xfel/metrology/legacy_scale/scale_core.cpp -text
xfel/metrology/legacy_scale/vector_collection.h -text
xfel/metrology/mark0.py -text
xfel/metrology/mark1.py -text
xfel/metrology/mark10.py -text
xfel/metrology/mark3.py -text
xfel/metrology/quadrant.py -text
xfel/metrology_ext.cpp -text
xfel/mono_simulation/SConscript -text
xfel/mono_simulation/__init__.py -text
xfel/mono_simulation/bandpass_gaussian.cpp -text
xfel/mono_simulation/bandpass_gaussian.h -text
xfel/mono_simulation/ccixfel_core.cpp -text
xfel/mono_simulation/ext.cpp -text
xfel/mono_simulation/max_like.py -text
xfel/mono_simulation/mono_treatment.py -text
xfel/mono_simulation/parameters.h -text
xfel/mono_simulation/util.py -text
xfel/mono_simulation/vector_collection.h -text
xfel/sacla/dump_sacla_data.py -text
xfel/sacla/mpccd_geom2json.py -text
xfel/small_cell/__init__.py -text
xfel/small_cell/small_cell.py -text
xfel/small_cell/solve_orientation.py -text
xfel/small_cell/write_orientation_arrows.py -text
xfel/ui/__init__.py -text
xfel/ui/command_line/__init__.py -text
xfel/ui/command_line/get_hit_timestamps.py -text
xfel/ui/command_line/plot_isoform_cloud.py -text
xfel/ui/command_line/plot_run_stats.py -text
xfel/ui/command_line/plot_uc_cloud.py -text
xfel/ui/command_line/print_run_stats.py -text
xfel/ui/command_line/xfel_gui_launch.py -text
xfel/ui/components/__init__.py -text
xfel/ui/components/icons/16x16/cancel.png -text
xfel/ui/components/icons/16x16/delete.png -text
xfel/ui/components/icons/16x16/info.png -text
xfel/ui/components/icons/16x16/led_alert.png -text
xfel/ui/components/icons/16x16/led_idle.png -text
xfel/ui/components/icons/16x16/led_off.png -text
xfel/ui/components/icons/16x16/led_on.png -text
xfel/ui/components/icons/16x16/open.png -text
xfel/ui/components/icons/16x16/run.png -text
xfel/ui/components/icons/16x16/stop.png -text
xfel/ui/components/icons/16x16/viewmag.png -text
xfel/ui/components/icons/24x24/def.png -text
xfel/ui/components/icons/24x24/gold_star.png -text
xfel/ui/components/icons/24x24/light_on.png -text
xfel/ui/components/icons/24x24/open.png -text
xfel/ui/components/icons/24x24/run.png -text
xfel/ui/components/icons/24x24/save.png -text
xfel/ui/components/icons/24x24/silver_star.png -text
xfel/ui/components/icons/24x24/term.png -text
xfel/ui/components/icons/24x24/txt.png -text
xfel/ui/components/icons/32x32/calib.png -text
xfel/ui/components/icons/32x32/check.png -text
xfel/ui/components/icons/32x32/config.png -text
xfel/ui/components/icons/32x32/convert.png -text
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xfel/ui/components/icons/32x32/info.png -text
xfel/ui/components/icons/32x32/list.png -text
xfel/ui/components/icons/32x32/open.png -text
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xfel/ui/components/icons/32x32/play.png -text
xfel/ui/components/icons/32x32/quick_restart.png -text
xfel/ui/components/icons/32x32/redo.png -text
xfel/ui/components/icons/32x32/run.png -text
xfel/ui/components/icons/32x32/search.png -text
xfel/ui/components/icons/32x32/settings.png -text
xfel/ui/components/icons/32x32/stop.png -text
xfel/ui/components/icons/32x32/test.png -text
xfel/ui/components/icons/32x32/txt.png -text
xfel/ui/components/icons/32x32/undo.png -text
xfel/ui/components/icons/32x32/write.png -text
xfel/ui/components/run_stats_plotter.py -text
xfel/ui/components/submission_tracker.py -text
xfel/ui/components/xfel_gui_controls.py -text
xfel/ui/components/xfel_gui_dialogs.py -text
xfel/ui/components/xfel_gui_init.py -text
xfel/ui/components/xfel_gui_plotter.py -text
xfel/ui/db/__init__.py -text
xfel/ui/db/cfgs/image_dict.cfg -text
xfel/ui/db/cfgs/index_all.cfg -text
xfel/ui/db/cfgs/submit.phil -text
xfel/ui/db/dxtbx_db.py -text
xfel/ui/db/experiment.py -text
xfel/ui/db/job.py -text
xfel/ui/db/run.py -text
xfel/ui/db/rungroup.py -text
xfel/ui/db/schema.sql -text
xfel/ui/db/stats.py -text
xfel/ui/db/tag.py -text
xfel/ui/db/trial.py -text
xfel/ui/db/xfel_db.py -text
xfel/ui/doc/NOTES.txt -text
xfel/util/cctbx_xfel_installer.py svneol=native#text/x-python
xfel/util/dials_pickle_reader.py -text
xfel/vonHamos/__init__.py -text
xfel/vonHamos/fit_3_gaussian.py -text
xfel/vonHamos/test_3_gaussian.py -text
xfel/vonHamos/xes_ext.cpp -text
xfel/xpp/__init__.py -text
xfel/xpp/cfgs/index_all.cfg -text
xfel/xpp/cfgs/submit.phil -text
xfel/xpp/experiment_schema.sql -text
xfel/xpp/isoform.py -text
xfel/xpp/progress_support.py -text
xfel/xpp/progress_utils.py -text
xfel/xpp/simulate.py -text
xfel/xpp/split_pickles.py -text
