id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10411 Bad sheet data wolfram.seifert@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description After using ISOLDE to improve my structure and save using the following command line: isolde write phenixRsrInput #1.2 2.4 #1.1 modelFileName TauB_refinement5_one_nucleotide_fixed.cif paramFileName TauB_refinement5_one_nucleotide_fixed.eff I got the following error and the regions that are not modelled in my structure now are filled with a line from the starting point of this region till the end of it. Bad sheet data. Please use Help / Report a Bug with this structure. Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/maps/W5_J202_localresolution.mrc Opened W5_J202_localresolution.mrc as #1, grid size 320,320,320, pixel 0.822, shown at level 0.128, step 2, values float32 > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement3/TauA_DNA_refinement2_ready_for_phenix_real_space_refined_000.cif Summary of feedback from opening C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement3/TauA_DNA_refinement2_ready_for_phenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 294 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""18"" near line 113 Bad residue range for struct_conf ""19"" near line 114 Bad residue range for struct_conf ""20"" near line 115 Bad residue range for struct_conf ""21"" near line 116 Bad residue range for struct_conf ""22"" near line 117 24 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauA_DNA_refinement2_ready_for_phenix_real_space_refined_000.cif #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available > volume #1 step 1 > select add #2 12264 atoms, 12711 bonds, 108 pseudobonds, 1373 residues, 2 models selected > hide sel atoms > show sel cartoons > volume #1 level 0.2 > dssp > dssp minStrandLen 2 > hide #!1 models > color sel bychain > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement2/TauA_DNA_emergencystructure.pdb Chain information for TauA_DNA_emergencystructure.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available > select subtract #2 Nothing selected > select add #3 12269 atoms, 12716 bonds, 1374 residues, 1 model selected > hide sel atoms > show sel cartoons > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > select subtract #3 Nothing selected > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1/TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif Summary of feedback from opening C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1/TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 159 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""13"" near line 106 Bad residue range for struct_conf ""14"" near line 107 Bad residue range for struct_conf ""15"" near line 108 Bad residue range for struct_conf ""16"" near line 109 Bad residue range for struct_conf ""17"" near line 110 29 messages similar to the above omitted Invalid residue range for struct_conf ""56"": invalid chain ""E"", near line 149 Invalid residue range for struct_conf ""57"": invalid chain ""E"", near line 150 Invalid residue range for struct_conf ""58"": invalid chain ""E"", near line 151 Invalid residue range for struct_conf ""59"": invalid chain ""E"", near line 152 Invalid residue range for struct_conf ""60"": invalid chain ""E"", near line 153 4 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif #4 --- Chain | Description B | No description available C | No description available D | No description available E | No description available > dssp minStrandLen 2 > hide #!3 models > hide #!2 models > color #!4 bychain > hide #!4 models > show #!3 models > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > close #4 > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > close #3 > close #1 > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/maps/W5_J202_localresolution.mrc Opened W5_J202_localresolution.mrc as #1, grid size 320,320,320, pixel 0.822, shown at level 0.128, step 2, values float32 > volume #1 step 1 > volume #1 level 0.1419 > volume #1 level 0.2 > volume #1 level 0.1459 > volume #1 level 0.2203 > select #2/E.F Expected an objects specifier or a keyword > select #2/E,F 1845 atoms, 2068 bonds, 108 pseudobonds, 90 residues, 2 models selected > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 1845 atom styles > select #2/E:1-6,40-45,D:1-6,39-45 259 atoms, 287 bonds, 13 residues, 1 model selected > select #2/E:1-6,40-45/D:1-6,39-45 338 atoms, 363 bonds, 25 residues, 1 model selected > select #2/E:1-6,40-45/F:1-6,39-45 511 atoms, 569 bonds, 28 pseudobonds, 25 residues, 2 models selected > select #2/E:1-6,40-45/F:1-6,40-45 492 atoms, 548 bonds, 28 pseudobonds, 24 residues, 2 models selected > delete sel > cd > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement3 Current working directory is: C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauA\Eustermann_method\J202_37Amap\Isolde_Alphafold_method\Refinement3 > save > TauA_DNA_refinement2_ready_for_phenix_real_space_refined_000_DNAtest.pdb #2 > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1/TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif Summary of feedback from opening C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1/TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 159 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""13"" near line 106 Bad residue range for struct_conf ""14"" near line 107 Bad residue range for struct_conf ""15"" near line 108 Bad residue range for struct_conf ""16"" near line 109 Bad residue range for struct_conf ""17"" near line 110 29 messages similar to the above omitted Invalid residue range for struct_conf ""56"": invalid chain ""E"", near line 149 Invalid residue range for struct_conf ""57"": invalid chain ""E"", near line 150 Invalid residue range for struct_conf ""58"": invalid chain ""E"", near line 151 Invalid residue range for struct_conf ""59"": invalid chain ""E"", near line 152 Invalid residue range for struct_conf ""60"": invalid chain ""E"", near line 153 4 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif #3 --- Chain | Description B | No description available C | No description available D | No description available E | No description available > hide #!2 models > hide #!1 models > dssp > show #!1 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > transparency Missing or invalid ""percent"" argument: Expected a number > transparency 50 > graphics silhouettes true > lighting soft > select #3/E:1-258 1977 atoms, 2033 bonds, 244 residues, 1 model selected > delete sel > cd > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1 Current working directory is: C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauA\Eustermann_method\J202_37Amap\Isolde_Alphafold_method\Refinement1 > save > TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000_deletedPhosphatasedomain.pdb > #3 > select #3/B 3483 atoms, 3548 bonds, 428 residues, 1 model selected > select #3/B:108-239 1106 atoms, 1127 bonds, 132 residues, 1 model selected > delete sel > select #3/D:17-39 174 atoms, 178 bonds, 23 residues, 1 model selected > select #3/D:17-34 134 atoms, 137 bonds, 18 residues, 1 model selected > color sel bychain > hide #!3 models > show #!3 models > select add #3 7390 atoms, 7538 bonds, 914 residues, 1 model selected > select subtract #3 Nothing selected > select subtract #3.1 Nothing selected > color #!3 bychain > select #3/D:17-34 134 atoms, 137 bonds, 18 residues, 1 model selected > delete sel > save > TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000_deletedPhosphatasedomain_deletedHelical_deletedt95Nterminus.pdb > #3 Cannot save 'TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000_deletedPhosphatasedomain_deletedHelical_deletedt95Nterminus.pdb': Unable to open file 'TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000_deletedPhosphatasedomain_deletedHelical_deletedt95Nterminus.pdb' for writing > save > TauA_refinement_deletedPhosphatasedomain_deletedHelical_deletedt95Nterminus.pdb > #3 > volume #1 level 0.3284 > select #3/C:17-34 Nothing selected > select #3/C:732-777 385 atoms, 393 bonds, 46 residues, 1 model selected > select #3/C:732-771 334 atoms, 341 bonds, 40 residues, 1 model selected > delete sel > volume #1 level 0.35 > select #3/B:431-443 100 atoms, 99 bonds, 13 residues, 1 model selected > delete sel > hide pseudobonds > select #3/D:248-252 41 atoms, 42 bonds, 5 residues, 1 model selected > delete sel > select #3/B:366-371 39 atoms, 38 bonds, 6 residues, 1 model selected > delete sel > select #3/B:403-416 126 atoms, 128 bonds, 14 residues, 1 model selected > delete sel > select #3/C:852-864 95 atoms, 94 bonds, 13 residues, 1 model selected > delete sel > select #3/E:413-419 58 atoms, 57 bonds, 7 residues, 1 model selected > delete sel > save TauA_refinement_1_trimmered.pdb #3 > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/maps/cryosparc_P43_J202_006_volume_map.mrc Opened cryosparc_P43_J202_006_volume_map.mrc as #4, grid size 320,320,320, pixel 0.822, shown at level 0.133, step 2, values float32 > volume #4 step 1 > volume #4 level 0.2218 > volume #4 level 0.3103 > hide #!1 models > hide #!3 models > volume #4 level 0.1619 > volume #4 level 0.2744 > close #3 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > set bgColor #ffffff00 > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > color #1/D:12-23/E:52-63 #7BBCD4 > color #1/I:12-23/J:52-63 #7BBCD4 > open 8CLI Summary of feedback from opening 8CLI fetched from pdb --- note | Fetching compressed mmCIF 8cli from http://files.rcsb.org/download/8cli.cif 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B hot pink > color #2/C dark salmon > color #2/D,E cornflower blue > color #2/D:16-26/E:15-25 #7BBCD4 > color #1/A:174-251 dark khaki > color #1/A:252-337 medium aquamarine > color #1/A:367-437 pale green > color #1/A:610-714 peru > color #1/D:12-23/E:52-63 #7BBCD4 > color #1/I:12-23/J:52-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,9.9226,0,1,0,24.621,0,0,1,23.909 > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > view matrix models #2,1,0,0,3.8688,0,1,0,12.837,0,0,1,82.529 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > color #1/D:12-23/E:52-63 #7BBCD4 > color #1/I:12-23/J:52-63 #7BBCD4 > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-23/E:52-63 #7BBCD4 > color #2/I:12-23/J:52-63 #7BBCD4 > graphics silhouettes true > turn > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6 > cartoon style nucleic xsection round width 2 thickness 0.4 > hide pseudobonds > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > ui mousemode right ""move picked models"" > view matrix models #1,1,0,0,7.878,0,1,0,-26.23,0,0,1,76.007 > view matrix models #2,1,0,0,-11.628,0,1,0,36.992,0,0,1,-110.99 > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.5306,-0.78095,0.32951,351.49,0.8162,-0.57561,-0.049919,200.68,0.22866,0.24246,0.94283,-187.81 > view matrix models > #2,-0.81677,0.37717,-0.4366,372.48,-0.57508,-0.59317,0.56341,316.85,-0.046478,0.71126,0.70139,-166.01 > view matrix models > #2,0.89101,-0.30795,-0.33356,153.08,-0.32579,-0.94544,0.002583,478.57,-0.31616,0.10637,-0.94272,416.3 > view matrix models > #2,-0.0127,0.97523,0.22083,-63.336,0.89332,-0.088156,0.44069,-32.364,0.44924,0.20287,-0.87007,232.55 > view matrix models > #2,-0.063644,0.97446,0.21537,-52.051,0.96206,0.0025385,0.27282,-21.122,0.2653,0.22456,-0.93765,280.52 > view matrix models > #2,0.26042,-0.089172,-0.96137,388.75,0.95438,-0.12686,0.27029,6.246,-0.14606,-0.9879,0.052067,347.71 > view matrix models > #2,0.32178,-0.90838,-0.26701,362.69,0.93868,0.26919,0.21543,-54.297,-0.12381,-0.31996,0.93931,-9.573 > ui mousemode right ""move picked models"" > view matrix models > #2,0.32178,-0.90838,-0.26701,366.6,0.93868,0.26919,0.21543,-74.593,-0.12381,-0.31996,0.93931,-14.546 > select subtract #2 Nothing selected > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #2/D:12-23/E:52-63 #7BBCD4 > color #2/D,E cornflower blue > color #2/D:12-23/E:52-63 #7BBCD4 > color #2/B dark salmon > color #2/C hot pink > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.50912,-0.85937,-0.047769,266.11,0.83753,0.48185,0.25762,-107.31,-0.19837,-0.17117,0.96507,-35.768 > select subtract #2 Nothing selected > ui mousemode right ""move picked models"" > view matrix models #1,1,0,0,6.4353,0,1,0,-35.571,0,0,1,105.96 > view matrix models > #2,0.50912,-0.85937,-0.047769,267.05,0.83753,0.48185,0.25762,-100.54,-0.19837,-0.17117,0.96507,-53.322 > ui mousemode right ""rotate selected models"" > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > view matrix models > #2,0.44933,-0.81697,-0.36147,348.94,0.094702,0.44589,-0.89006,336.82,0.88833,0.3657,0.27772,-193.93 > view matrix models > #2,0.42489,-0.82246,-0.37819,358.89,-0.024891,0.407,-0.91309,373.11,0.9049,0.39738,0.15246,-171.86 > select subtract #2 Nothing selected > select add #1 15002 atoms, 15478 bonds, 97 pseudobonds, 1747 residues, 2 models selected > view matrix models > #1,0.89759,-0.049527,-0.43805,126.53,-0.43638,0.041047,-0.89882,431.01,0.062497,0.99793,0.015231,91.106 > select subtract #1 Nothing selected > ui mousemode right ""move picked models"" > view matrix models > #1,0.89759,-0.049527,-0.43805,125.27,-0.43638,0.041047,-0.89882,416.7,0.062497,0.99793,0.015231,110.8 > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.43689,-0.82036,-0.36897,353.87,0.043174,0.42884,-0.90235,353.11,0.89848,0.3783,0.22278,-184.55 > view matrix models > #2,0.66092,-0.54187,-0.5192,294.26,-0.063366,0.64908,-0.75808,294.33,0.74778,0.53393,0.39465,-229.17 > view matrix models > #2,0.65957,-0.54218,-0.52059,294.93,-0.070903,0.64463,-0.7612,297.43,0.74829,0.53897,0.38674,-228.27 > view matrix models > #2,0.67833,-0.60729,-0.41361,277.2,-0.024673,0.54377,-0.83887,327.75,0.73435,0.57923,0.35387,-225.21 > ui mousemode right ""move picked models"" > view matrix models > #2,0.67833,-0.60729,-0.41361,279.68,-0.024673,0.54377,-0.83887,336.71,0.73435,0.57923,0.35387,-217.36 > select subtract #2 Nothing selected > select add #1 15002 atoms, 15478 bonds, 97 pseudobonds, 1747 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.89847,-0.046385,-0.43657,124.15,-0.43443,0.04959,-0.89934,414.67,0.063365,0.99769,0.024404,108.8 > view matrix models > #1,0.89429,-0.061344,-0.44326,129.41,-0.44357,0.0092854,-0.89619,424.08,0.059092,0.99807,-0.018906,118.45 > view matrix models > #1,0.76824,0.071463,-0.63616,166.25,-0.64006,0.068662,-0.76525,423.17,-0.011007,0.99508,0.09849,108.57 > select subtract #1 Nothing selected > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > view matrix models > #2,0.69153,-0.60185,-0.39946,272.53,0.016661,0.56615,-0.82414,320.72,0.72216,0.56326,0.40153,-223.87 > ui mousemode right ""move picked models"" > view matrix models > #2,0.69153,-0.60185,-0.39946,269.78,0.016661,0.56615,-0.82414,313.96,0.72216,0.56326,0.40153,-225.17 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.68059,-0.60634,-0.41128,275.71,-0.017676,0.54759,-0.83656,327.28,0.73245,0.57662,0.36197,-219.83 > select subtract #2 Nothing selected > ui mousemode right ""move picked models"" > view matrix models > #1,0.76824,0.071463,-0.63616,163.66,-0.64006,0.068662,-0.76525,416.92,-0.011007,0.99508,0.09849,107.12 > ui mousemode right ""move picked models"" > view matrix models > #2,0.68059,-0.60634,-0.41128,280.52,-0.017676,0.54759,-0.83656,308.13,0.73245,0.57662,0.36197,-153.97 > ui mousemode right ""rotate selected models"" > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > view matrix models > #2,0.62557,-0.63112,-0.45864,307.79,-0.1784,0.45657,-0.87162,365.49,0.7595,0.62708,0.17302,-121.6 > view matrix models > #2,0.69258,-0.60142,-0.39828,274,0.020013,0.56794,-0.82283,293.48,0.72107,0.5619,0.40538,-159.81 > view matrix models > #2,0.68294,-0.56001,-0.46901,285.51,-0.073114,0.58644,-0.80669,303.67,0.7268,0.58521,0.35956,-153.96 > ui mousemode right ""move picked models"" > view matrix models > #2,0.68294,-0.56001,-0.46901,283.41,-0.073114,0.58644,-0.80669,298.59,0.7268,0.58521,0.35956,-155.13 > select subtract #2 Nothing selected > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.66009,-0.65879,-0.36095,279.95,0.021187,0.49664,-0.8677,313.36,0.75089,0.56511,0.34178,-151.37 > select subtract #2 Nothing selected > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > view matrix models > #2,0.68468,-0.54753,-0.48108,283.66,-0.084401,0.59605,-0.7985,296.82,0.72394,0.58732,0.36189,-155.58 > select subtract #2 Nothing selected > cd C:/Users/wseif/Desktop/Publication/yTFIIIC/Fig1 Current working directory is: C:\Users\wseif\Desktop\Publication\yTFIIIC\Fig1 > save > C:/Users/wseif/Desktop/Publication/yTFIIIC/Fig1/yeastTauB_humanTauB_DNAbindingcomparison.cxs > includeMaps true > ui mousemode right ""move picked models"" > mmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cli, chain A (#2) with TauB_refinement5_for_fenix_real_space_refined_000.cif, chain A (#1), sequence alignment score = 355 RMSD between 47 pruned atom pairs is 1.251 angstroms; (across all 406 pairs: 14.798) > mmaker #1/A to #2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cli, chain A (#2) with TauB_refinement5_for_fenix_real_space_refined_000.cif, chain A (#1), sequence alignment score = 355 RMSD between 47 pruned atom pairs is 1.251 angstroms; (across all 406 pairs: 14.798) > mmaker #1/A:108-172 to #2/A:174-251 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cli, chain A (#2) with TauB_refinement5_for_fenix_real_space_refined_000.cif, chain A (#1), sequence alignment score = 82.6 RMSD between 49 pruned atom pairs is 0.983 angstroms; (across all 65 pairs: 2.709) > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > mmaker #1/ to #2/A:174-251 > matchmaker #1/ to #2/A:174-251 Missing required ""to"" argument > mmaker #1/D to #2/D Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cli, chain D (#2) with TauB_refinement5_for_fenix_real_space_refined_000.cif, chain D (#1), sequence alignment score = 61.6 RMSD between 14 pruned atom pairs is 1.114 angstroms; (across all 35 pairs: 3.979) > show #!2 models > select add #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.59878,-0.79284,-0.11348,255.78,-0.2541,-0.32242,0.91186,79.485,-0.75954,-0.51716,-0.39451,534.15 > ui mousemode right ""move picked models"" > view matrix models > #1,0.89939,0.4192,0.12398,-102.88,-0.051407,-0.18021,0.98228,51.634,0.43411,-0.88983,-0.14053,312.9 > mmaker #1/D,E to #2/D,E Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cli, chain E (#2) with TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1), sequence alignment score = 61.6 RMSD between 15 pruned atom pairs is 1.138 angstroms; (across all 35 pairs: 3.962) > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.84918,0.22286,0.47879,186.39,0.48426,-0.033099,0.8743,-109.08,0.21069,0.97429,-0.079813,-21.927 > view matrix models > #2,0.53298,0.3055,0.78905,-172.49,0.00070306,-0.9327,0.36064,288.1,0.84613,-0.19166,-0.49733,188.67 > view matrix models > #2,0.61912,-0.7779,-0.10754,247.47,-0.30469,-0.36417,0.88008,105.31,-0.72378,-0.51211,-0.46249,543.36 > select subtract #2 Nothing selected > select add #1 15002 atoms, 15478 bonds, 97 pseudobonds, 1747 residues, 2 models selected > view matrix models > #1,-0.69668,0.47505,0.53755,117.14,0.35846,-0.41856,0.83446,47.073,0.62141,0.77404,0.12131,-100.06 > view matrix models > #1,0.91297,0.4027,0.065745,-83.894,0.051481,-0.27352,0.96049,51.036,0.40477,-0.87351,-0.27045,361.12 > ui mousemode right ""move picked models"" > view matrix models > #1,0.91297,0.4027,0.065745,-77.261,0.051481,-0.27352,0.96049,47.039,0.40477,-0.87351,-0.27045,333.5 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.86094,0.50695,-0.042157,-66.4,-0.037053,0.14514,0.98872,-27.589,0.50735,-0.84966,0.14374,223.55 > view matrix models > #1,0.99368,-0.11135,-0.013889,29.051,0.012305,-0.014894,0.99981,-6.576,-0.11154,-0.99367,-0.013429,405.73 > view matrix models > #1,0.99948,-0.032177,-0.0020105,9.2131,0.001278,-0.022767,0.99974,-2.7995,-0.032215,-0.99922,-0.022714,393.36 > mmaker #1/D:16-26/E:15-25 to #2/D:12-23/E:52-63 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cli, chain E (#2) with TauB_refinement5_for_fenix_real_space_refined_000.cif, chain D (#1), sequence alignment score = 34.2 RMSD between 11 pruned atom pairs is 0.762 angstroms; (across all 11 pairs: 0.762) > select subtract #1 Nothing selected > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > close #2 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-23/E:52-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > mmaker #2/D:12-23/E:52-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6 > cartoon style nucleic xsection round width 2 thickness 0.4 > hide pseudobonds > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-23/E:52-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > mmaker #2/D:12-23/E:52-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > cartoon style width 1.5 thickness 0.3 > cartoon style helix width 1.5 thickness 0.3 > cartoon style strand xsection rectangle width 2 > hide #!2 models > ribbon style x rect > ribbon style (#1 & coil) x oval > cartoon style protein modeHelix default arrows false xsection oval width 1 > thickness 1 > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > cartoon style protein modeHelix default arrows false xsection oval width 3 > thickness 3 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > select #2 transparency 60 Expected a keyword > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 60 > hide #!1 models > hide pseudobonds > transparency 60 > transparency 60 sel cartoons Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency sel cartoons 60 Missing or invalid ""percent"" argument: Expected a number > transparency sel 60 cartoons > hide #!2 models > show #!1 models > show #!2 models > select subtract #2 Nothing selected > transparency sel 50 cartoons > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 40 cartoons > select subtract #2 Nothing selected > mmaker #2/B to #1/C Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain C (#1) with 8cli, chain B (#2), sequence alignment score = 225.6 RMSD between 94 pruned atom pairs is 1.161 angstroms; (across all 508 pairs: 10.994) > mmaker #2/C to #1/B Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain B (#1) with 8cli, chain C (#2), sequence alignment score = 328.6 RMSD between 212 pruned atom pairs is 1.159 angstroms; (across all 454 pairs: 10.624) > hide #!2 models > show #!2 models > color #2 grey > mmaker #2/D:12-23/E:52-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > nucleotides stubs > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6 > cartoon style nucleic xsection round width 2 thickness 0.4 > hide pseudobonds > cartoon style protein modeHelix default arrows false xsection oval width 3 > thickness 3 > close #2 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-23/E:52-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > mmaker #2/D:12-23/E:52-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > hide #!1 models > mmaker #2/D:12-23/E:52-63 > matchmaker #2/D:12-23/E:52-63 Missing required ""to"" argument > select #2/D:12-23/E:52-63 492 atoms, 550 bonds, 32 pseudobonds, 24 residues, 2 models selected Alignment identifier is 2/D Alignment identifier is 2/E > show #!1 models > close #1 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > cartoon style thickness 2.5 > lighting soft > silhouette width 1.5 Unknown command: silhouette width 1.5 > hide #!2 models > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > lighting soft > silhouette width 0.5 Unknown command: silhouette width 0.5 > graphics silhouettes false > graphics silhouettes true > silhouettes width 0.5 Unknown command: silhouettes width 0.5 > graphics silhouettes width 0.5 > graphics silhouettes width 1.5 > graphics silhouettes width 2 > cartoon style thickness 2.5 > cartoon style thickness 1.5 > cartoon style thickness 3 > cartoon style thickness 2 > cartoon style thickness 2.5 > show #!2 models > hide #!2 models > close #2 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > select #2/B,C#3/B,C 10099 atoms, 10376 bonds, 13 pseudobonds, 1270 residues, 3 models selected > show #!2 models > hide #!2 models > select #2/B,C#1/B,C 19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected > show #!2 models > hide #!2 models > hide sel > hide sel cartoons > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > select add #1 25101 atoms, 25854 bonds, 110 pseudobonds, 3017 residues, 5 models selected > select add #2 30957 atoms, 31946 bonds, 205 pseudobonds, 3629 residues, 6 models selected > select subtract #1 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > select subtract #2 Nothing selected > select clear > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 60 cartoons > select clear > hide pseudobonds > show ribbons > select #2/B,C#1/B,C 19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected > hide sel cartoons > select clear > cartoon style protein modeHelix tube radius 2 sides 24 vvvvvv Expected a keyword > cartoon style protein modeHelix tube radius 2 sides 24 > hide #!2 models > close #2 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > hide pseudobonds > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > select #2/B,C#1/B,C 19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected > hide sel cartoons > select clear > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 60 cartoons > select clear > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 40 cartoons > select clear > view > view matrix view matrix camera -0.24397,0.003917,-0.96977,-160.33,0.26193,-0.96256,-0.069782,168.08,-0.93374,-0.27104,0.23381,293.51 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 [Repeated 2 time(s)] > view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0l Invalid ""models"" argument: Require numeric values > view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0 > view initial #1 > view position mod > #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 Missing or invalid ""models"" argument: invalid models specifier > view position > #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 Missing or invalid ""models"" argument: only initial part ""#1,1,0,0,0,0,1,0,0,0,0,1,0"" of atom specifier valid > view matrix models #1 Invalid ""models"" argument: Expected model id and 12 comma-separated numbers > view matrix models #1 Invalid ""models"" argument: Expected model id and 12 comma-separated numbers > view matrix models #1 Invalid ""models"" argument: Expected model id and 12 comma-separated numbers > view matrix view matrix camera -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 > > -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42 Unknown command: -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42 > view > -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42 Expected an objects specifier or a view name or a keyword > view matrix > -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42 Expected a keyword > view matrix camera > -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42 [Repeated 2 time(s)] > view matrix view matrix camera -0.33132,0.081403,-0.94,12.509,0.24498,-0.95469,-0.16902,163.33,-0.91116,-0.28627,0.29637,273.03 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > -0.33132,0.081403,-0.94,12.509,0.24498,-0.95469,-0.16902,163.33,-0.91116,-0.28627,0.29637,273.03 > hide #!2 models > select #1/A:1-107,173-668#2/A:1-173,252-714 7676 atoms, 7788 bonds, 4 pseudobonds, 946 residues, 3 models selected > hide sel cartoons > select clear > show #!2 models > select #1/A:1-107,173-668#2/A:1-173,252-715 7682 atoms, 7794 bonds, 4 pseudobonds, 947 residues, 3 models selected > hide sel cartoons > select clear > select clearcccselect #1/A:1-107,173-668#2/A:1-173,252-716 Expected an objects specifier or a keyword > hide sel cartoons > select clear > select #1/A:1-107,173-668#2/A:1-173,252-716 7690 atoms, 7802 bonds, 4 pseudobonds, 948 residues, 3 models selected > hide sel cartoons > select clear > hide #!2 models > show #!2 models > color #2/A:174-251 grey > select #1/A:1-107,173-668#2/A:1-173,252-716/D,E 9125 atoms, 9410 bonds, 95 pseudobonds, 1018 residues, 4 models selected > hide sel cartoons > select clear > select #1/A:1-107,173-668#2/A:1-173,252-716/D,E 9125 atoms, 9410 bonds, 95 pseudobonds, 1018 residues, 4 models selected > hide sel cartoons > hide atoms > select clear > select #1/D,E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > select add #1 15002 atoms, 15478 bonds, 97 pseudobonds, 1747 residues, 2 models selected > select cleaer Expected an objects specifier or a keyword > select clear > select #1/A:1-107,173-668/D:1-14,32-40/E:1-11,27-40#2/A:1-173,252-716/D,E 10108 atoms, 10509 bonds, 152 pseudobonds, 1066 residues, 5 models selected > hide sel cartoons > hide sel atoms > select clear > view matrix view matrix camera -0.24482,-0.01464,-0.96946,53.443,0.27457,-0.96001,-0.05484,185.79,-0.92988,-0.2796,0.23905,254.21 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix view matrix camera -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > hide pseudobonds > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > select #2/B,C#1/B,C 19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected > hide sel cartoons > select clear > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 40 cartoons > select clear > Focus on th Wh2 domain Unknown command: Focus on th Wh2 domain > > -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83 Unknown command: -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83 > let's hide the other domains and DNA Unknown command: let's hide the other domains and DNA > select #1/A:1-107,173-668/D:1-14,32-40/E:1-11,27-40#2/A:1-173,252-716/D,E 10108 atoms, 10509 bonds, 152 pseudobonds, 1066 residues, 5 models selected > hide sel cartoons > hide sel atoms > select clear > color #2/A:174-251 grey > view matrix > -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83 Expected a keyword > view matrix camera > -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > hide pseudobonds > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > select #2/B,C#1/B,C 19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected > hide sel cartoons > select clear > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 40 cartoons > select clear > view matrix camera > -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83 > let's hide the other domains and DNA Unknown command: let's hide the other domains and DNA > select #1/A:1-107,173-668/D:1-14,32-40/E:1-11,27-40#2/A:1-173,252-716/D,E 10108 atoms, 10509 bonds, 152 pseudobonds, 1066 residues, 5 models selected > hide sel cartoons > hide sel atoms > select clear > color #2/A:174-251 grey > cd > C:/Users/wseif/Desktop/Publication/yTFIIIC/Fig_comparison_yeast_human_TauB_DNA_interactions Current working directory is: C:\Users\wseif\Desktop\Publication\yTFIIIC\Fig_comparison_yeast_human_TauB_DNA_interactions > save WH2_zoomin_comparison_WS_01.png width 7200 transparentBackground true > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > hide pseudobonds > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > select #2/B,C#1/B,C 19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected > hide sel cartoons > select clear > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 40 cartoons > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > view matrix view matrix camera -0.40992,-0.71131,-0.57097,119.39,0.50216,-0.69857,0.50974,254.91,-0.76145,-0.077771,0.64355,338.88 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 > hide #!2 models > view matrix camera > -0.40992,-0.71131,-0.57097,119.39,0.50216,-0.69857,0.50974,254.91,-0.76145,-0.077771,0.64355,338.88 > select #1/A:1-184,262-668/D:1-24/E:16-40#2/A:1-251,338-716/D,E 10049 atoms, 10463 bonds, 148 pseudobonds, 1060 residues, 5 models selected > hide sel cartoons > hide sel atoms > select clear > show #!2 models > hide #!2 models > color #2/A:252-337 grey > show #!2 models > show #1/E:16 > show #1/E:16 cartoons > show #1/E:16-20 cartoons > show #1/D:22-25 cartoons > show #1/D:22-25 atoms > show #1/E:16-20 atoms > show #1/D:22-25 atoms > show #1/D:21-25 atoms > show #1/D:21-25 cartoons > view matrix view matrix camera -0.36384,-0.71791,-0.59348,105.42,0.076066,-0.65793,0.74923,300.71,-0.92835,0.22745,0.294,291.68 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 > save WH3_zoomin_comparison_WS_01.png width 7200 transparentBackground true > close #2 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > hide pseudobonds > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > select #2/B,C#1/B,C 19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected > hide sel cartoons > select clear > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 40 cartoons > select clear > view matrix view matrix camera -0.34791,0.044606,-0.93646,-123.99,0.30379,-0.93961,-0.15762,142.25,-0.88694,-0.33933,0.31335,313.94 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0 > close > open > C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > open 8CLI 8cli title: TFIIIC TauB-DNA monomer [more info...] Chain information for 8cli #2 --- Chain | Description | UniProt A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109 B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822 C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911 D | DNA (35-MER) | E | DNA (35-MER) | Non-standard residues in 8cli #2 --- ZN — zinc ion > dssp minStrandLen 2 > color #2/A forest green > color #2/B dark salmon > color #2/C hot pink > color #2/D,E cornflower blue > color #2/A:174-251 dark khaki > color #2/A:252-337 medium aquamarine > color #2/A:367-437 pale green > color #2/A:610-714 peru > color #2/D:12-22/E:53-63 #7BBCD4 > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > select #2/D-E 1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected > show sel atoms > style sel stick Changed 1435 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > hide pseudobonds > mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1) with 8cli, chain D (#2), sequence alignment score = 34.2 RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs: 1.244) > select #2/B,C#1/B,C 19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected > hide sel cartoons > select clear > select #2 15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected > transparency sel 40 cartoons > select clear > view matrix camera > -0.34791,0.044606,-0.93646,-123.99,0.30379,-0.93961,-0.15762,142.25,-0.88694,-0.33933,0.31335,313.94 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1/A:1-333,417-668/D:1-13,28-40/E:1-13,28-40#2/A:1-366,438-716/D,E 10080 atoms, 10494 bonds, 160 pseudobonds, 1059 residues, 5 models selected > hide sel cartoons > hide sel atoms > select clear > color #2/A:367-437 grey > show #!2 models > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/W6_J290_monomer_localresolution.mrc Opened W6_J290_monomer_localresolution.mrc as #3, grid size 480,480,480, pixel 0.822, shown at level 0.0492, step 2, values float32 > volume #3 step 1 > volume #3 level 1.351 > transparency 60 > volume #3 level 0.5833 > volume #3 level 1.251 > volume #3 level 1.017 > hide #!3 models > show #!3 models > hide #!3 models > view matrix view matrix camera 0.014841,0.2777,0.96055,330.44,-0.41972,-0.8702,0.25806,213.9,0.90753,-0.40699,0.10364,221.52 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0 > close #3 > close > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/W6_J290_monomer_localresolution.mrc Opened W6_J290_monomer_localresolution.mrc as #2, grid size 480,480,480, pixel 0.822, shown at level 0.0492, step 2, values float32 > clipper associate #2 toModel #1 Opened W6_J290_monomer_localresolution.mrc as #1.1.1.1, grid size 480,480,480, pixel 0.822, shown at level 1.14, step 1, values float32 Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available > volume #1.1.1.1 level 0.8469 > close > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > set bgColor white > lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1 > hide atoms > show ribbons > dssp minStrandLen 2 > cartoon style thickness 2.5 > graphics silhouettes width 1.5 > color #1/A forest green > color #1/B hot pink > color #1/C dark salmon > color #1/D,E cornflower blue > color #1/D:16-26/E:15-25 #7BBCD4 > color #1/A:108-172 dark khaki > color #1/A:185-262 medium aquamarine > color #1/A:334-416 pale green > color #1/A:550-640 peru > select #1/D-E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > show sel atoms > style sel stick Changed 1640 atom styles > show sel atoms > nucleotides sel tube/slab shape muffler > select clear > close > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif Summary of feedback from opening C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 268 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""25"" near line 119 Bad residue range for struct_conf ""26"" near line 120 Bad residue range for struct_conf ""32"" near line 126 Bad residue range for struct_conf ""33"" near line 127 Bad residue range for struct_conf ""34"" near line 128 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/W6_J290_monomer_localresolution.mrc Opened W6_J290_monomer_localresolution.mrc as #2, grid size 480,480,480, pixel 0.822, shown at level 0.0492, step 2, values float32 > clipper associate #2 toModel #1 Opened W6_J290_monomer_localresolution.mrc as #1.1.1.1, grid size 480,480,480, pixel 0.822, shown at level 1.14, step 1, values float32 Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available > select #1/D 817 atoms, 916 bonds, 40 residues, 1 model selected > 16 Unknown command: 16 > select #1/D 817 atoms, 916 bonds, 40 residues, 1 model selected > 16view sel Unknown command: 16view sel > view sel > select #1/D:16 21 atoms, 23 bonds, 1 residue, 1 model selected > view sel > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 66 residues in model #1.2 to IUPAC-IUB standards. Done loading forcefield > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > isolde restrain basepairs sel > select #1/D,E 1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected > isolde sim start /D-E Sim termination reason: None ISOLDE: stopped sim > addh #1.2 Summary of feedback from adding hydrogens to TauB_refinement5_for_fenix_real_space_refined_000.cif #1.2 --- warnings | Not adding hydrogens to /D DA 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /E DG 1 P because it is missing heavy-atom bond partners notes | No usable SEQRES records for TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain A; guessing termini instead No usable SEQRES records for TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain B; guessing termini instead No usable SEQRES records for TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain C; guessing termini instead No usable SEQRES records for TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain D; guessing termini instead No usable SEQRES records for TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain E; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1, /B SER 156, /C MET 1 Chain-initial residues that are not actual N termini: /A VAL 322, /A LYS 538 Chain-final residues that are actual C termini: /A ARG 668, /B SER 685, /C MET 588 Chain-final residues that are not actual C termini: /A ILE 262, /A SER 477 1716 hydrogen bonds Adding 'H' to /A VAL 322 Adding 'H' to /A LYS 538 14315 hydrogens added > isolde sim start /D-E ISOLDE: started sim > select #1/D:16 32 atoms, 34 bonds, 1 residue, 1 model selected > isolde stepto /D:21 > isolde stepto next [Repeated 3 time(s)] > volume #1.1.1.1 level 0.5526 > volume #1.1.1.1 level 0.8697 > volume #1.1.1.1 level 0.6861 > volume #1.1.1.1 level 0.9198 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/D:16 32 atoms, 34 bonds, 1 residue, 1 model selected > view sel > cd > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5 Current working directory is: C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5 > isolde write phenixRsrInput #1.2 2.4 #1.1 modelFileName > TauB_refinement5_one_nucleotide_fixed.cif paramFileName > TauB_refinement5_one_nucleotide_fixed.eff > dssp #1.2 > save TauB_refinement5_one_nucleotide_fixed.cif #1.2 selectedOnly true > bestGuess true computedSheets true The `computedSheets true` option requires the `pprintpp` module to be installed, but this is missing in the ChimeraX 1.7 release. Use the command: pip install pprintpp on the ChimeraX command line to install it, then try again. > pip install pprintpp > open > C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_one_nucleotide_fixed.cif Chain information for TauB_refinement5_one_nucleotide_fixed.cif #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > hide #!1 models > hide #!1.1 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > hide #1.3 models > hide #!2 atoms > show #!2 cartoons > close #2 > hide #!1 models > show #!1 models > show #!1.2 models > show #1.3 models > show #!1.1 models > save test.pdb #1.2 > isolde write phenixRsrInput #1.2 2.4 #1.1 modelFileName > TauB_refinement5_one_nucleotide_fixed.cif paramFileName > TauB_refinement5_one_nucleotide_fixed.eff > dssp #1.2 > save TauB_refinement5_one_nucleotide_fixed.cif #1.2 selectedOnly true > bestGuess true computedSheets true Bad sheet data. Please use Help / Report a Bug with this structure. A phenix.real_space_refine input file TauB_refinement5_one_nucleotide_fixed.eff with settings recommended for ISOLDE models has been written to C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5 along with a current snapshot of your model (TauB_refinement5_one_nucleotide_fixed.cif). You can start a refinement job by running the following command in the working directory: phenix.real_space_refine TauB_refinement5_one_nucleotide_fixed.eff. OpenGL version: 3.3.0 NVIDIA 532.09 OpenGL renderer: NVIDIA GeForce RTX 2070 Super/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_DE.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Alienware Model: Alienware m15 R3 OS: Microsoft Windows 11 Home (Build 22621) Memory: 16,929,841,152 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 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PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1 File attachment: TauB_refinement5_one_nucleotide_fixed.cif }}} [attachment:""TauB_refinement5_one_nucleotide_fixed.cif""] " defect closed normal Input/Output duplicate Greg Couch all ChimeraX