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Data from Phenix projects, such as scripts used for publications.
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Improvement of cryo-EM maps by density modification.
T. C. Terwilliger, S. J. Ludtke, R. J. Read, P. D. Adams, P. V. Afonine.
Nat Methods 17, 923–927 (2020).
doi:10.1038/s41592-020-0914-9.
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Macromolecular x-ray structure determination using weak, single-wavelength anomalous data.
G. Bunkóczi, A. J. McCoy, N. Echols, R. W. Grosse-Kunstleve, P. D. Adams, J. M. Holton, R. J. Read, T. C. Terwilliger.
Nat Methods 12, 127–130 (2015).
doi:10.1038/nmeth.3212.
Find the spreadsheets used in the analyses in this paper and the scaled, merged data used in Fig. 2.
- 000README
- adaptors_version_2014-05-19.tgz
- au_update_2014_05-24b.tgz
- cysz_merged_scaled_data_2014-06-05.tgz
- SD1_Fig1AB_hyss_llgc_vs_correlation_r.xlsx
- SD2_Fig2AB_CysZ_merging_hyss_j_rerun_with_unbiased.xlsx
- SD3_Fig3AB_S6_S7_Fig3C_S1_S2_autobuild_r.xlsx
- FigS3_holton_challenge_finding_sites_h.xlsx
- SD5_FigS4_CysZ_phaser_vs_correlation_scoring_anom_signal_2014-06-25.xlsx
- SD6_FigS5_llg_scoring_merge_123_2014-06-29.xlsx
- SD7_FigS8_holton_challenge_diff_fourier_2014-06-10h.xlsx
- SD8_Scaled_merged_datasets_for_Figs2AB_cysz_merged_scaled_data_2014-06-05.tgz
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Decision-making in structure solution using bayesian estimates of map quality: the PHENIX AutoSol wizard.
T. C. Terwilliger, P. D. Adams, R. J. Read, A. J. McCoy, N. W. Moriarty, R. W. Grosse-Kunstleve, P. V. Afonine, P. H. Zwart, L. W. Hung.
Acta Crystallogr D Biol Crystallogr 65, 582–601 (2009).
doi:10.1107/S0907444909012098.
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Ligand identification using electron-density map correlations.
T. C. Terwilliger, P. D. Adams, N. W. Moriarty, J. D. Cohn.
Acta Crystallogr D Biol Crystallogr 63, 101–107 (2007).
doi:10.1107/S0907444906046233.
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Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models.
T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, P. D. Adams, N. W. Moriarty, P. Zwart, R. J. Read, D. Turk, L. W. Hung.
Acta Crystallogr D Biol Crystallogr 63, 597–610 (2007).
doi:10.1107/S0907444907009791.
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FEM: feature-enhanced map.
P. V. Afonine, N. W. Moriarty, M. Mustyakimov, O. V. Sobolev, T. C. Terwilliger, D. Turk, A. Urzhumtsev, P. D. Adams.
Acta Crystallogr D Biol Crystallogr 71, 646–666 (2015).
doi:10.1107/S1399004714028132.
- fig_10_rho_and_kurtosis_vs_bsharp.tar.gz
- fig_11_unsharp_bsharp_alltoget.tar.gz
- fig_12_HE_illustration.tar.gz
- fig_13_HE_effect_on_maps.tar.gz
- fig_14_HE_effect_on_map2.tar.gz
- fig_15_HE_1d_example.tar.gz
- fig_16_choosing_contours.tar.gz
- fig_17_results_1F8T.tar.gz
- fig_18_19_results_1NH2.tar.gz
- fig_1_fem_protocol.tar.gz
- fig_20_neutron_2r24.tar.gz
- fig_21_results_2G38.tar.gz
- fig_22_bad_lig_1SE6.tar.gz
- fig_23_sharp_2VUI_2PPI.tar.gz
- fig_24_25_26_rsr_3I9Q.tar.gz
- fig_2abcd_missing_data.tar.gz
- fig_3abcd_weights.tar.gz
- fig_4_shelx_weight.tar.gz
- fig_5_low_density.tar.gz
- fig_6_omit_protocol.tar.gz
- fig_7_omit_test.tar.gz
- fig_8_kurtosis_bsharp_dmin.tar.gz
- fig_9_kurtosis_illustrations.tar.gz
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Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.
P. A. Janowski, N. W. Moriarty, B. P. Kelley, D. A. Case, D. M. York, P. D. Adams, G. L. Warren.
Acta Crystallogr D Struct Biol 72, 1062–1072 (2016).
doi:10.1107/S2059798316012225.
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Polder maps: improving OMIT maps by excluding bulk solvent.
D. Liebschner, P. V. Afonine, N. W. Moriarty, B. K. Poon, O. V. Sobolev, T. C. Terwilliger, P. D. Adams.
Acta Crystallogr D Struct Biol 73, 148–157 (2017).
doi:10.1107/S2059798316018210.