id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9069 fitmap: mismatch coordinate array sizes chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/wkeliason/Downloads/cryosparc_P5_J167_005_volume_map_sharp_RNA- > DNA-Hybrid (1).mrc"" format mrc Opened cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc as #1, grid size 360,360,360, pixel 0.97, shown at level 0.0899, step 2, values float32 > select add #1 2 models selected > ui tool show ""Volume Viewer"" > volume #1 style mesh > vop gaussian #1 sdev 2.91 Opened cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian as #2, grid size 360,360,360, pixel 0.97, shown at step 1, values float32 > volume #2 level 0.07036 > open /Users/wkeliason/Downloads/ChimeraX/PDB/GsDnaB_Xray/4esv.pdb.gz 4esv.pdb.gz title: A new twist on the translocation mechanism of helicases from the structure of DNAb with its substrates [more info...] Chain information for 4esv.pdb.gz #3 --- Chain | Description | UniProt A B C D E F G H I J K L | DNAB | Q9X4C9_GEOSE 1-445 1-454 V | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | W | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | Non-standard residues in 4esv.pdb.gz #3 --- ALF — tetrafluoroaluminate ion CA — calcium ion GDP — guanosine-5'-diphosphate MES — 2-(N-morpholino)-ethanesulfonic acid > delete /F,G,H,I,J,K,L,W > show atoms > hide atoms > show cartoons > ui tool show ""Model Panel"" > select subtract #1 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-24.384,0,1,0,110.09,0,0,1,37.302 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.99863,-0.05072,0.01313,-22.395,0.047412,0.98151,0.18545,89.137,-0.022293,-0.18457,0.98257,52.366 > view matrix models > #3,0.76771,-0.090839,0.63433,-55.072,0.010973,0.99162,0.12872,97.462,-0.64071,-0.091861,0.76227,128.98 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.76771,-0.090839,0.63433,45.001,0.010973,0.99162,0.12872,107.41,-0.64071,-0.091861,0.76227,152.1 > view matrix models > #3,0.76771,-0.090839,0.63433,47.306,0.010973,0.99162,0.12872,111.24,-0.64071,-0.091861,0.76227,160.87 > view matrix models > #3,0.76771,-0.090839,0.63433,46.798,0.010973,0.99162,0.12872,111.37,-0.64071,-0.091861,0.76227,164.59 > ui tool show ""Model Panel"" > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.76771,-0.090839,0.63433,47.51,0.010973,0.99162,0.12872,111.14,-0.64071,-0.091861,0.76227,173.13 > view matrix models > #3,0.76771,-0.090839,0.63433,42.915,0.010973,0.99162,0.12872,110.79,-0.64071,-0.091861,0.76227,172.68 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.78639,0.08113,0.61238,32.662,-0.1083,0.99409,0.0073778,133.88,-0.60816,-0.072124,0.79053,165.59 > view matrix models > #3,0.80403,0.10572,0.58512,31.961,-0.15798,0.98668,0.038817,136.34,-0.57322,-0.12365,0.81002,163.41 > view matrix models > #3,0.84389,0.047588,0.5344,36.265,-0.03823,0.99886,-0.028577,129.97,-0.53515,0.003686,0.84475,148.64 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.84389,0.047588,0.5344,37.25,-0.03823,0.99886,-0.028577,137.05,-0.53515,0.003686,0.84475,147.28 > fitmap #3 inMap #2 Fit molecule 4esv.pdb.gz (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 16995 atoms average map value = 0.05238, steps = 120 shifted from previous position = 10.8 rotated from previous position = 10.5 degrees atoms outside contour = 12015, contour level = 0.07036 Position of 4esv.pdb.gz (#3) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.77401095 -0.09468342 0.62605279 34.64323104 0.07311972 0.99550712 0.06015876 109.46615004 -0.62893605 -0.00078674 0.77745664 164.38128436 Axis -0.04807855 0.99003283 0.13237617 Axis point 228.24251148 0.00000000 17.18775591 Rotation angle (degrees) 39.33190824 Shift along axis 128.46965059 > show #!1 models > volume #1 level 0.09829 > hide #!1 models > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.77401,-0.094683,0.62605,35.003,0.07312,0.99551,0.060159,109.75,-0.62894,-0.00078674,0.77746,165.8 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.96934,0.037867,0.24279,43.349,0.19996,-0.69582,-0.68982,270.01,0.14282,0.71722,-0.68205,181.84 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.96934,0.037867,0.24279,44.636,0.19996,-0.69582,-0.68982,253.09,0.14282,0.71722,-0.68205,188.87 > view matrix models > #3,0.96934,0.037867,0.24279,45.345,0.19996,-0.69582,-0.68982,254.81,0.14282,0.71722,-0.68205,190.7 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.75786,0.17932,0.62728,21.851,0.11659,0.90878,-0.40065,138.6,-0.64191,0.37677,0.66783,163.27 > select subtract #3 Nothing selected > ui mousemode right ""translate selected models"" > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.75786,0.17932,0.62728,22.78,0.11659,0.90878,-0.40065,151.19,-0.64191,0.37677,0.66783,162.73 > view matrix models > #3,0.75786,0.17932,0.62728,24.865,0.11659,0.90878,-0.40065,157.94,-0.64191,0.37677,0.66783,160.8 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.74396,-0.0063526,0.6682,33.7,0.24405,0.93346,-0.26285,130.85,-0.62207,0.35862,0.696,157.29 > view matrix models > #3,0.71667,0.025423,0.69695,31.799,0.10455,0.98413,-0.14341,130.5,-0.68953,0.17564,0.70263,174.51 > view matrix models > #3,0.7133,-0.26596,0.64843,54.373,0.70084,0.26503,-0.66225,163.3,0.0042769,0.92684,0.37544,90.35 > view matrix models > #3,0.41297,-0.47152,0.77918,84.555,0.55479,-0.54824,-0.62581,223.84,0.72226,0.69072,0.035191,64.975 > view matrix models > #3,0.23106,-0.37425,0.89808,85.651,0.09997,-0.90904,-0.40454,270.38,0.96779,0.18325,-0.17263,90.774 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.23106,-0.37425,0.89808,88.901,0.09997,-0.90904,-0.40454,258.51,0.96779,0.18325,-0.17263,84.301 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.23697,-0.25597,0.93719,77.468,-0.128,-0.96448,-0.23106,268.36,0.96305,-0.065208,-0.26131,108.16 > view matrix models > #3,0.33348,-0.13034,0.9337,60.545,-0.62113,-0.77543,0.1136,273.77,0.70922,-0.61783,-0.33955,174.35 > view matrix models > #3,0.35638,-0.12275,0.92624,58.499,-0.60564,-0.78522,0.12897,271.39,0.71147,-0.60693,-0.35418,174.83 > view matrix models > #3,0.86523,-0.0059913,0.50134,40.455,-0.0048302,0.99978,0.020284,113.26,-0.50135,-0.019972,0.86501,145.97 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.86523,-0.0059913,0.50134,42.039,-0.0048302,0.99978,0.020284,124.31,-0.50135,-0.019972,0.86501,147.01 > color #3 #942192ff > view matrix models > #3,0.86523,-0.0059913,0.50134,43.213,-0.0048302,0.99978,0.020284,125.98,-0.50135,-0.019972,0.86501,148.52 > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.79156,-0.040803,0.60973,42.527,0.014941,0.99876,0.04744,121.54,-0.61091,-0.028441,0.79119,166.86 > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.7572,-0.021548,0.65283,40.749,0.034885,0.99936,-0.0074758,124.65,-0.65225,0.028434,0.75747,170.68 > view matrix models > #3,0.82345,0.19715,0.53203,32.166,-0.12665,0.9779,-0.16635,156.92,-0.55307,0.069598,0.83022,151.49 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.82345,0.19715,0.53203,19.036,-0.12665,0.9779,-0.16635,153.94,-0.55307,0.069598,0.83022,149.98 > view matrix models > #3,0.82345,0.19715,0.53203,20.671,-0.12665,0.9779,-0.16635,155.06,-0.55307,0.069598,0.83022,149.03 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.86926,0.34415,0.3549,23.753,-0.26742,0.93113,-0.24794,179.56,-0.41579,0.12062,0.90143,125.59 > view matrix models > #3,0.93943,0.19883,0.27919,32.671,-0.092853,0.93172,-0.35111,171.78,-0.32993,0.30392,0.89374,106.62 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.93943,0.19883,0.27919,37.936,-0.092853,0.93172,-0.35111,179.83,-0.32993,0.30392,0.89374,108.03 > view matrix models > #3,0.93943,0.19883,0.27919,37.093,-0.092853,0.93172,-0.35111,180.24,-0.32993,0.30392,0.89374,109.49 > select subtract #3 Nothing selected > hide #!3 models > show #!3 models > hide #!2 models > ui mousemode right ""rotate selected models"" > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ui mousemode right ""translate selected models"" > hide #!2 models > show #!2 models > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.93943,0.19883,0.27919,36.776,-0.092853,0.93172,-0.35111,174.34,-0.32993,0.30392,0.89374,111.34 > select subtract #3 Nothing selected > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.95563,0.12863,0.26501,40.752,0.029521,0.85329,-0.52061,182.76,-0.29309,0.50533,0.81163,103.12 > view matrix models > #3,0.88804,-0.15886,0.43145,49.375,0.31808,0.88988,-0.32702,133.67,-0.33199,0.42764,0.84078,108.99 > view matrix models > #3,0.89354,-0.14479,0.42499,48.576,0.30489,0.89053,-0.33763,135.94,-0.32958,0.43126,0.83987,108.61 > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.91619,-0.018991,0.4003,40.989,-0.25484,0.74329,0.61853,111.19,-0.30928,-0.6687,0.67615,188.72 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.91619,-0.018991,0.4003,41.955,-0.25484,0.74329,0.61853,108.84,-0.30928,-0.6687,0.67615,180.77 > select subtract #3 Nothing selected > hide #!3 models > show #!3 models > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.91619,-0.018991,0.4003,48.757,-0.25484,0.74329,0.61853,109.5,-0.30928,-0.6687,0.67615,183.54 > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.91619,-0.018991,0.4003,47.872,-0.25484,0.74329,0.61853,109.88,-0.30928,-0.6687,0.67615,184.94 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.86996,0.19172,0.45432,34.625,-0.48887,0.45605,0.74366,138.94,-0.064623,-0.86906,0.49047,190.1 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.86996,0.19172,0.45432,37.205,-0.48887,0.45605,0.74366,139.08,-0.064623,-0.86906,0.49047,185.18 > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > view matrix models > #3,0.86996,0.19172,0.45432,37.032,-0.48887,0.45605,0.74366,141.59,-0.064623,-0.86906,0.49047,184.56 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.76022,0.38928,0.52013,29.812,-0.085894,0.8538,-0.51346,194.91,-0.64397,0.34567,0.68251,150.55 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.76022,0.38928,0.52013,30.827,-0.085894,0.8538,-0.51346,194.11,-0.64397,0.34567,0.68251,156.35 > view matrix models > #3,0.76022,0.38928,0.52013,32.158,-0.085894,0.8538,-0.51346,193.88,-0.64397,0.34567,0.68251,164.09 > hide #!2 models > select subtract #3 Nothing selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ui mousemode right ""rotate selected models"" > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.68769,0.064897,0.7231,40.096,0.16437,0.95622,-0.24214,137.32,-0.70715,0.28538,0.64691,177.38 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.68769,0.064897,0.7231,32.288,0.16437,0.95622,-0.24214,136.56,-0.70715,0.28538,0.64691,177.98 > select subtract #3 Nothing selected > hide #!3 models > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > cartoon #2 > show #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.41195,0.19399,0.89032,36.28,-0.77028,0.59612,0.22652,207.73,-0.48679,-0.77911,0.395,244.25 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.41195,0.19399,0.89032,37.207,-0.77028,0.59612,0.22652,204.62,-0.48679,-0.77911,0.395,237.33 > view matrix models > #3,0.41195,0.19399,0.89032,33.326,-0.77028,0.59612,0.22652,208.27,-0.48679,-0.77911,0.395,232.82 > hide #!3 models > surface style #2 solid > transparency #2.1 50 > show #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.6246,0.39515,0.67359,20.195,-0.75732,0.51702,0.39894,195.65,-0.19062,-0.7593,0.62219,180.84 > view matrix models > #3,0.71557,0.33835,0.61113,20.424,-0.63508,0.67947,0.36742,176.55,-0.29093,-0.65103,0.70108,176.88 > view matrix models > #3,0.65554,0.37915,0.65307,20.003,-0.72065,0.57255,0.39097,189.37,-0.22568,-0.72693,0.64856,179.9 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.65554,0.37915,0.65307,26.247,-0.72065,0.57255,0.39097,186.78,-0.22568,-0.72693,0.64856,170.92 > view matrix models > #3,0.65554,0.37915,0.65307,25.803,-0.72065,0.57255,0.39097,185.72,-0.22568,-0.72693,0.64856,171.31 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.73448,0.26534,0.6246,27.513,-0.62553,0.62162,0.47149,165.72,-0.26316,-0.73701,0.62255,178.09 > view matrix models > #3,0.73988,0.34589,0.57701,26.536,-0.45749,0.88754,0.054586,171.84,-0.49324,-0.30436,0.81491,156.74 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.73988,0.34589,0.57701,26.378,-0.45749,0.88754,0.054586,164.06,-0.49324,-0.30436,0.81491,168.4 > view matrix models > #3,0.73988,0.34589,0.57701,27.546,-0.45749,0.88754,0.054586,170.65,-0.49324,-0.30436,0.81491,169.95 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.78637,0.39963,0.47108,29.561,-0.090895,0.82912,-0.55163,194.39,-0.61103,0.39097,0.68832,151.3 > view matrix models > #3,0.80925,0.14867,0.56834,33.422,0.086968,0.92647,-0.36618,153.4,-0.58099,0.34576,0.73681,146.52 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.80925,0.14867,0.56834,34.168,0.086968,0.92647,-0.36618,160.25,-0.58099,0.34576,0.73681,147.64 > hide #!2 models > show #!2 models > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.75383,0.36502,0.54636,28.608,0.58892,-0.7441,-0.31542,206.94,0.29141,0.55953,-0.77589,189.26 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.75383,0.36502,0.54636,30.685,0.58892,-0.7441,-0.31542,184.62,0.29141,0.55953,-0.77589,188.79 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.82104,0.31768,0.47431,33.604,0.52676,-0.74183,-0.41498,200,0.22003,0.59057,-0.77641,194.07 > view matrix models > #3,0.79571,0.13105,0.59133,36.514,0.4743,-0.74199,-0.4738,210.74,0.37667,0.65747,-0.65257,162.81 > select /B 3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected > view matrix models > #3,0.82364,0.18478,0.53616,35.629,0.52044,-0.62187,-0.58517,209.26,0.2253,0.76101,-0.60836,167.47 > view matrix models > #3,0.64453,0.14444,0.75081,35.844,0.029097,-0.98591,0.1647,210.18,0.76403,-0.084306,-0.63965,168.05 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.64453,0.14444,0.75081,29.15,0.029097,-0.98591,0.1647,199.77,0.76403,-0.084306,-0.63965,165.35 > view matrix models > #3,0.64453,0.14444,0.75081,30.133,0.029097,-0.98591,0.1647,199.88,0.76403,-0.084306,-0.63965,162.01 > show #!1 models > hide #!1 models > select add #2 3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 4 models selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 5 models selected > select subtract #3 2 models selected > hide #!3 models > surface style #2 solid > transparency #2.1 50 > transparency #2.1 100 > transparency #2.1 60 > show #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.99958,0.0023976,-0.029041,4.8268,-0.002289,0.99999,0.0037706,-0.26881,0.02905,-0.0037025,0.99957,-4.3647 > select subtract #2 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.69628,0.36934,0.61545,23.981,0.64997,0.03935,-0.75894,162.16,-0.30453,0.92846,-0.21266,167.03 > view matrix models > #3,0.63372,0.34764,0.69105,24.461,0.7541,-0.078497,-0.65205,148.94,-0.17243,0.93434,-0.3119,162.8 > view matrix models > #3,0.48003,0.34765,0.80542,29.074,0.86527,-0.036436,-0.49998,121.07,-0.14447,0.93692,-0.3183,160.45 > view matrix models > #3,0.57993,0.35536,0.73307,25.419,0.79648,-0.058238,-0.60186,138.79,-0.17119,0.93291,-0.31681,163.22 > view matrix models > #3,0.47319,0.33303,0.81558,29.693,0.84441,-0.43535,-0.31215,129.81,0.2511,0.8364,-0.48722,142.94 > view matrix models > #3,0.49578,0.34394,0.79744,28.477,0.86313,-0.2966,-0.4087,128.55,0.095955,0.89092,-0.44391,151.04 > view matrix models > #3,0.77527,0.24059,0.58401,26.871,0.62501,-0.42565,-0.65435,183.1,0.091152,0.87232,-0.48037,156.06 > view matrix models > #3,0.74842,0.030337,0.66254,34.97,0.61599,-0.40206,-0.67743,184.73,0.24583,0.91511,-0.31959,123 > view matrix models > #3,0.50945,0.35383,0.78439,27.735,-0.73968,0.64585,0.18908,175.11,-0.43969,-0.67653,0.59075,202.81 > view matrix models > #3,0.72597,0.18254,0.66306,27.913,-0.64019,0.53159,0.55459,137.93,-0.25124,-0.8271,0.50278,201.4 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.72597,0.18254,0.66306,32.841,-0.64019,0.53159,0.55459,161.64,-0.25124,-0.8271,0.50278,195.31 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.73055,0.18368,0.65769,32.818,-0.62847,0.55753,0.54239,160.04,-0.26706,-0.80958,0.52274,193.95 > view matrix models > #3,0.75612,0.3673,0.54164,29.976,-0.64637,0.54868,0.53025,163.5,-0.10242,-0.75103,0.65228,161.87 > view matrix models > #3,0.91746,0.18817,0.3505,42.662,0.051554,0.81739,-0.57378,180.93,-0.39447,0.54449,0.74022,104.06 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.91746,0.18817,0.3505,44.333,0.051554,0.81739,-0.57378,199.03,-0.39447,0.54449,0.74022,111.15 > select subtract #3 Nothing selected > ui mousemode right ""rotate selected models"" > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.82674,-0.088875,0.55553,51.018,0.32328,0.88319,-0.33981,146.06,-0.46043,0.46052,0.7589,121.08 > view matrix models > #3,0.84579,-0.047728,0.53138,48.88,0.28696,0.88035,-0.37768,153.4,-0.44977,0.47192,0.75828,119.38 > view matrix models > #3,0.77669,-0.22695,0.58758,61.393,0.62172,0.42594,-0.6573,173.8,-0.1011,0.87582,0.47192,86.893 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.77669,-0.22695,0.58758,54.699,0.62172,0.42594,-0.6573,153.5,-0.1011,0.87582,0.47192,88.831 > view matrix models > #3,0.77669,-0.22695,0.58758,54.724,0.62172,0.42594,-0.6573,151.84,-0.1011,0.87582,0.47192,95.498 > view matrix models > #3,0.77669,-0.22695,0.58758,48.001,0.62172,0.42594,-0.6573,149.73,-0.1011,0.87582,0.47192,94.225 > ui tool show ""Fit in Map"" > fitmap #3 inMap #2 Fit molecule 4esv.pdb.gz (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 16995 atoms average map value = 0.04866, steps = 200 shifted from previous position = 5.51 rotated from previous position = 25.2 degrees atoms outside contour = 12337, contour level = 0.07036 Position of 4esv.pdb.gz (#3) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.73705548 -0.25928832 0.62411441 46.54334356 0.56774984 0.73851176 -0.36367637 110.90652387 -0.36661880 0.62239052 0.69153504 107.97414385 Axis 0.60712692 0.61000000 0.50921204 Axis point 17.84925748 0.00000000 79.73037780 Rotation angle (degrees) 54.29929976 Shift along axis 150.89243060 > hide #!3 models > show #!3 models > hide #!3 models > volume #2 level 0.08867 > surface style #2 solid > transparency #2 50 > transparency #2 40 > surface style #2 solid > select add #2 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 5 models selected > select subtract #3 2 models selected > transparency #2.1 50 > transparency #2.1 40 > transparency #2.1 80 > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 5 models selected > show #!3 models > select subtract #2 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.74875,-0.27548,0.60289,48.224,0.56467,0.74144,-0.36249,111.1,-0.34715,0.61186,0.71072,106.87 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.6152,-0.50595,0.6046,75.373,0.72602,0.66251,-0.18434,83.147,-0.30728,0.55236,0.77491,100.5 > view matrix models > #3,0.79581,0.096124,0.59786,21.434,0.34402,0.74074,-0.57702,153.21,-0.49833,0.66488,0.55642,133.15 > view matrix models > #3,0.81777,0.11395,0.56415,21.318,0.12473,0.92182,-0.36699,144.41,-0.56186,0.37048,0.73963,140.22 > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.77859,0.16429,0.60564,18.282,-0.030016,0.97377,-0.22556,143.45,-0.62681,0.15744,0.7631,157.44 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.77859,0.16429,0.60564,21.059,-0.030016,0.97377,-0.22556,154.18,-0.62681,0.15744,0.7631,161.56 > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.77859,0.16429,0.60564,20.842,-0.030016,0.97377,-0.22556,161.95,-0.62681,0.15744,0.7631,171.65 > select subtract #3 Nothing selected > select add #3 16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected > view matrix models > #3,0.77859,0.16429,0.60564,22.946,-0.030016,0.97377,-0.22556,170.23,-0.62681,0.15744,0.7631,176.45 > select subtract #3 Nothing selected > select /V 280 atoms, 307 bonds, 14 residues, 1 model selected > color sel red > hide #!3 models > select /V 280 atoms, 307 bonds, 14 residues, 1 model selected > cartoon #2 > show #!3 models > hide #!3 models > show #!3 models > delete /v > lighting simple > lighting shadows true > lighting soft > hide #!2 models > show #!2 models > select add #3 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > view matrix models > #3,0.77859,0.16429,0.60564,24.43,-0.030016,0.97377,-0.22556,150.73,-0.62681,0.15744,0.7631,162.81 > view matrix models > #3,0.77859,0.16429,0.60564,23.161,-0.030016,0.97377,-0.22556,157.09,-0.62681,0.15744,0.7631,161.28 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.67008,-0.090884,0.73671,37.211,0.14357,0.9896,-0.0084999,118.52,-0.72827,0.11146,0.67616,182.32 > fitmap #3 inMap #2 Fit molecule 4esv.pdb.gz (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 16715 atoms average map value = 0.05205, steps = 116 shifted from previous position = 10.1 rotated from previous position = 11.9 degrees atoms outside contour = 14723, contour level = 0.088672 Position of 4esv.pdb.gz (#3) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.77427283 -0.09859350 0.62512472 34.91206194 0.07661590 0.99512778 0.06205406 109.12031465 -0.62819710 -0.00015228 0.77805423 164.37435490 Axis -0.04909590 0.98917515 0.13828275 Axis point 227.55345512 0.00000000 16.19159201 Rotation angle (degrees) 39.31020189 Shift along axis 128.95520228 > fitmap #3 inMap #2 Fit molecule 4esv.pdb.gz (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 16715 atoms average map value = 0.05205, steps = 36 shifted from previous position = 0.00277 rotated from previous position = 0.0141 degrees atoms outside contour = 14724, contour level = 0.088672 Position of 4esv.pdb.gz (#3) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.77414897 -0.09876516 0.62525101 34.91852212 0.07675219 0.99511076 0.06215848 109.09729217 -0.62833310 -0.00013054 0.77794441 164.39640167 Axis -0.04914928 0.98914318 0.13849233 Axis point 227.49227834 0.00000000 16.18924699 Rotation angle (degrees) 39.32153728 Shift along axis 128.96426304 Average map value = 0.05205 for 16715 atoms, 14724 outside contour > select subtract #3 Nothing selected > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > view matrix models > #3,0.79065,-0.11184,0.60197,36.373,0.13083,0.99133,0.012349,108.61,-0.59813,0.068991,0.79843,154.94 > view matrix models > #3,0.74028,-0.29228,0.60544,52.028,-0.35501,-0.9347,-0.01717,276.77,0.57093,-0.20223,-0.7957,204.07 > hide #!2 models > view matrix models > #3,0.77287,-0.33857,0.5367,58.024,-0.21507,0.65596,0.72351,96.906,-0.59701,-0.6746,0.43415,234.08 > show #!2 models > select /A/B/C/D/E 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > ui tool show ""Basic Actions"" > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 16540 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > view matrix models > #3,0.6688,-0.31806,0.67196,54.482,-0.35738,0.65503,0.66575,116.47,-0.65191,-0.6854,0.32442,250.41 > view matrix models > #3,0.55023,-0.51777,0.6551,80.01,-0.23541,0.65653,0.71662,99.531,-0.80114,-0.54852,0.23936,264.8 > view matrix models > #3,0.70899,0.20915,0.67349,18.167,0.26354,-0.9644,0.022056,213.76,0.65413,0.16186,-0.73887,168.28 > view matrix models > #3,0.53089,0.3275,0.78161,18.529,0.67755,-0.71801,-0.15936,174.56,0.50901,0.61417,-0.60307,142.4 > view matrix models > #3,0.4429,0.30822,0.84193,22.81,0.80749,-0.54521,-0.22519,157.26,0.38961,0.77958,-0.49036,133.63 > view matrix models > #3,0.22663,-0.39531,0.89015,82.718,0.34195,0.88805,0.30731,66.288,-0.91198,0.23474,0.33643,218.92 > view matrix models > #3,0.7246,-0.50097,0.47326,78.643,-0.32775,0.35359,0.8761,112.31,-0.60624,-0.78994,0.092017,273.94 > view matrix models > #3,0.96295,-0.098254,0.25116,51.124,-0.26356,-0.54037,0.79908,167.7,0.057208,-0.83567,-0.54624,270.43 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > view matrix models > #3,0.94174,0.13247,0.30916,33.733,-0.057996,-0.84145,0.53721,190.11,0.33131,-0.52384,-0.78475,246.44 > view matrix models > #3,0.84253,0.37453,0.38713,21.527,0.0707,-0.78938,0.60983,167.39,0.53399,-0.48643,-0.69155,215.36 > view matrix models > #3,0.63119,0.14831,0.76132,21.409,-0.22907,-0.90212,0.36566,226.79,0.74103,-0.40519,-0.53543,175.3 > view matrix models > #3,0.50389,0.51593,0.69275,17.99,-0.85733,0.39646,0.32833,213.32,-0.10525,-0.75936,0.6421,171.07 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.50389,0.51593,0.69275,22.627,-0.85733,0.39646,0.32833,209.26,-0.10525,-0.75936,0.6421,171.59 > view matrix models > #3,0.50389,0.51593,0.69275,33.904,-0.85733,0.39646,0.32833,214.26,-0.10525,-0.75936,0.6421,163.38 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.50723,0.84425,0.17307,61.994,-0.81381,0.40313,0.41857,201.12,0.28361,-0.35316,0.89154,76.742 > view matrix models > #3,0.67498,0.73168,0.095128,59.493,-0.71996,0.62492,0.30187,189.15,0.16143,-0.27225,0.94859,78.604 > view matrix models > #3,0.73282,0.67397,0.093443,57.434,-0.66233,0.67513,0.32484,178.22,0.15585,-0.29994,0.94114,81.542 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.73282,0.67397,0.093443,60.338,-0.66233,0.67513,0.32484,181,0.15585,-0.29994,0.94114,76.709 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.78363,0.61128,0.11077,57.509,-0.5941,0.68528,0.42124,164.63,0.18159,-0.3959,0.90016,83.835 > view matrix models > #3,0.76957,0.48443,0.41605,38.178,-0.62354,0.71057,0.32602,174.88,-0.1377,-0.51032,0.84889,127.28 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.76957,0.48443,0.41605,39.789,-0.62354,0.71057,0.32602,175.03,-0.1377,-0.51032,0.84889,133.23 > view matrix models > #3,0.76957,0.48443,0.41605,38.931,-0.62354,0.71057,0.32602,175.39,-0.1377,-0.51032,0.84889,133.66 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.78512,-0.35494,0.50754,80.098,0.59799,0.22111,-0.7704,186.33,0.16122,0.90837,0.38585,60.574 > view matrix models > #3,0.51984,-0.40841,0.75031,87.041,0.27816,-0.74952,-0.6007,261.49,0.80771,0.52098,-0.27603,81.811 > view matrix models > #3,0.52409,-0.47827,0.70469,95.138,0.2356,-0.71372,-0.65962,269.03,0.81843,0.51172,-0.26138,79.946 > view matrix models > #3,0.28753,-0.55343,0.78169,116.02,0.32522,-0.71125,-0.62319,256.59,0.90087,0.4334,-0.024518,54.459 > view matrix models > #3,0.28386,-0.60263,0.74583,122.73,0.28165,-0.69111,-0.66561,263.64,0.91657,0.39901,-0.026449,55.182 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.28386,-0.60263,0.74583,121.41,0.28165,-0.69111,-0.66561,264.62,0.91657,0.39901,-0.026449,57.601 > view matrix models > #3,0.28386,-0.60263,0.74583,111.88,0.28165,-0.69111,-0.66561,241.51,0.91657,0.39901,-0.026449,66.246 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.19418,-0.020926,0.98074,63.355,-0.68749,-0.71607,0.12084,265.84,0.69975,-0.69771,-0.15344,166.55 > view matrix models > #3,0.13483,0.2596,0.95626,54.401,-0.52931,-0.79697,0.29099,239.22,0.83765,-0.54539,0.029948,126.47 > view matrix models > #3,0.13526,0.291,0.94711,53.294,-0.50638,-0.80132,0.31853,234.64,0.85164,-0.52268,0.03897,122.85 > view matrix models > #3,-0.074076,0.34924,0.9341,71.721,-0.5898,-0.77064,0.24135,248.24,0.80415,-0.53305,0.26307,107.3 > view matrix models > #3,0.18255,0.60669,0.77369,45.503,-0.80206,-0.36325,0.47408,222.73,0.56866,-0.70709,0.42029,126.63 > ui mousemode right ""move picked models"" > view matrix models > #2,0.99958,0.0023976,-0.029041,2.3053,-0.002289,0.99999,0.0037706,1.5128,0.02905,-0.0037025,0.99957,-2.0813 > select subtract #3 Nothing selected > select add #3 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > view matrix models > #3,0.18255,0.60669,0.77369,-1.364,-0.80206,-0.36325,0.47408,164.12,0.56866,-0.70709,0.42029,159.87 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.18255,0.60669,0.77369,3.4731,-0.80206,-0.36325,0.47408,158.82,0.56866,-0.70709,0.42029,80.097 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.52562,0.022188,0.85043,-2.0361,-0.84729,-0.076083,0.52566,140.96,0.076366,-0.99685,-0.021191,187.8 > view matrix models > #3,0.70514,0.068068,0.7058,-9.1591,0.13903,0.96279,-0.23175,50.322,-0.69531,0.26155,0.66943,123.13 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.70514,0.068068,0.7058,-1.1567,0.13903,0.96279,-0.23175,140.09,-0.69531,0.26155,0.66943,173.46 > view matrix models > #3,0.70514,0.068068,0.7058,-1.4915,0.13903,0.96279,-0.23175,137.99,-0.69531,0.26155,0.66943,174.42 > view matrix models > #3,0.70514,0.068068,0.7058,16.888,0.13903,0.96279,-0.23175,135.45,-0.69531,0.26155,0.66943,176.94 > view matrix models > #3,0.70514,0.068068,0.7058,17.43,0.13903,0.96279,-0.23175,141.1,-0.69531,0.26155,0.66943,175.46 > fitmap #3 inMap #2 Fit molecule 4esv.pdb.gz (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 16715 atoms average map value = 0.05205, steps = 184 shifted from previous position = 9.64 rotated from previous position = 19.7 degrees atoms outside contour = 14724, contour level = 0.088672 Position of 4esv.pdb.gz (#3) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.77427187 -0.09860007 0.62512487 34.91407469 0.07662472 0.99512712 0.06205359 109.11924009 -0.62819719 -0.00014633 0.77805415 164.37478168 Axis -0.04909075 0.98917374 0.13829467 Axis point 227.55226949 0.00000000 16.18928083 Rotation angle (degrees) 39.31027841 Shift along axis 128.95608459 > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > select clear > sel:A Unknown command: sel:A > sel/A Unknown command: sel/A > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 4esv.pdb.gz (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 3286 atoms average map value = 0.05931, steps = 300 shifted from previous position = 28.2 rotated from previous position = 31.8 degrees atoms outside contour = 2828, contour level = 0.088672 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.73014,0.05375,0.68118,22.368,-0.093022,0.99544,0.021162,131.54,-0.67693,-0.078816,0.73181,180.25 > view matrix models > #3,0.58401,0.19074,0.78902,18.446,0.74153,0.2701,-0.61415,152.27,-0.33026,0.94375,0.016303,150.16 > select /B 3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected > hide #!2 models > view matrix models > #3,0.48391,0.52076,0.70331,16.223,0.79719,-0.59385,-0.1088,152.36,0.361,0.61332,-0.70251,168.79 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > view matrix models > #3,0.13217,0.05584,0.98965,52.798,0.99059,0.02839,-0.1339,97.53,-0.035573,0.99804,-0.051562,123.94 > show #!2 models > hide #!2 models > view matrix models > #3,0.65823,-0.53979,0.52475,80.326,-0.036274,0.6735,0.7383,78.684,-0.75195,-0.505,0.42373,242.45 > view matrix models > #3,0.89289,-0.22835,0.38807,50.778,-0.36505,0.1374,0.92079,127.01,-0.26358,-0.96383,0.039327,257.86 > show #!2 models > hide #!2 models > view matrix models > #3,0.76911,-0.4217,0.48025,66.266,-0.020828,0.73449,0.6783,79.023,-0.63878,-0.53169,0.55612,220.5 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > view matrix models > #3,0.89454,0.044908,0.44472,28.649,-0.41681,-0.27557,0.86622,162.45,0.16145,-0.96023,-0.22779,240.38 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > view matrix models > #3,0.64793,0.30508,0.69793,13.619,0.09381,-0.94127,0.32436,202.96,0.7559,-0.14469,-0.6385,169.92 > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > view matrix models > #3,0.87946,-0.12917,0.45811,39.524,-0.15405,-0.98791,0.017179,259.05,0.45036,-0.08568,-0.88873,219.96 > hide #!2 models > view matrix models > #3,-0.1975,-0.65819,-0.72649,289.14,0.77154,0.35282,-0.52939,136.34,0.60476,-0.66506,0.43814,116.27 > view matrix models > #3,0.92694,-0.1748,0.33202,49.359,-0.23281,-0.96187,0.14356,253.48,0.29426,-0.21037,-0.93229,247.12 > show #!2 models > hide #!2 models > show #!2 models > view matrix models > #3,0.93639,-0.071022,0.3437,40.996,-0.10911,-0.98969,0.09274,247.65,0.33357,-0.12434,-0.93449,238.18 > view matrix models > #3,0.22026,0.735,0.64129,35.084,0.28332,0.58089,-0.76308,192.65,-0.93339,0.34977,-0.080299,255.27 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.22026,0.735,0.64129,40.849,0.28332,0.58089,-0.76308,191.81,-0.93339,0.34977,-0.080299,264.37 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.58166,0.72477,0.3693,30.984,-0.029172,0.4723,-0.88096,240.44,-0.81291,0.50165,0.29586,208.06 > view matrix models > #3,0.54276,0.041705,0.83885,32.754,-0.57229,0.74939,0.33303,164.19,-0.61474,-0.66082,0.4306,246.8 > view matrix models > #3,0.55594,-0.048294,0.82982,37.783,-0.55438,0.72231,0.41344,156.57,-0.61936,-0.68988,0.37479,254.24 > view matrix models > #3,0.36803,-0.50803,0.77876,89.254,0.86583,-0.11807,-0.48621,150.87,0.33896,0.85321,0.39641,62.946 > view matrix models > #3,0.36965,-0.50795,0.77804,89.155,0.86735,-0.1117,-0.485,150.22,0.33327,0.85411,0.39928,63.188 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > view matrix models > #3,0.58881,-0.085349,0.80375,39.215,-0.38676,0.84343,0.37289,136.32,-0.70973,-0.53042,0.46361,245.19 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.58881,-0.085349,0.80375,42.016,-0.38676,0.84343,0.37289,136.55,-0.70973,-0.53042,0.46361,234.88 > view matrix models > #3,0.58881,-0.085349,0.80375,43.968,-0.38676,0.84343,0.37289,136.83,-0.70973,-0.53042,0.46361,235.47 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.50172,-0.40411,0.76483,75.698,0.38539,-0.68715,-0.61588,245.87,0.77444,0.60376,-0.18902,79.851 > view matrix models > #3,0.48021,-0.60975,0.63056,102.91,0.39422,-0.49216,-0.77613,248.04,0.78358,0.62128,0.0040348,59.87 > view matrix models > #3,0.36348,0.82972,0.42361,45.911,-0.84146,0.48753,-0.23291,260.16,-0.39978,-0.27179,0.87539,150.53 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.36348,0.82972,0.42361,52.339,-0.84146,0.48753,-0.23291,268.95,-0.39978,-0.27179,0.87539,151.34 > view matrix models > #3,0.36348,0.82972,0.42361,55.78,-0.84146,0.48753,-0.23291,266.85,-0.39978,-0.27179,0.87539,144.2 > select add #3 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > select subtract #3 Nothing selected > select add #3 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > view matrix models > #3,0.36348,0.82972,0.42361,33.124,-0.84146,0.48753,-0.23291,382.51,-0.39978,-0.27179,0.87539,122.73 > view matrix models > #3,0.36348,0.82972,0.42361,54.294,-0.84146,0.48753,-0.23291,371.3,-0.39978,-0.27179,0.87539,127.66 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.82706,0.078404,0.55662,41.764,-0.30907,0.89054,0.33379,241.03,-0.46953,-0.44809,0.76076,156.03 > view matrix models > #3,0.69891,-0.13556,0.70225,53.959,-0.61391,-0.61746,0.4918,348.6,0.36694,-0.77484,-0.51476,211.95 > view matrix models > #3,0.56613,0.038898,0.8234,45.184,0.24756,-0.9608,-0.12482,341.6,0.78626,0.2745,-0.55357,109.9 > view matrix models > #3,0.5764,-0.0081112,0.81713,47.62,0.7149,-0.47937,-0.50904,301.68,0.39584,0.87757,-0.27051,85.425 > view matrix models > #3,0.6191,0.1162,0.77667,39.567,0.68582,0.40181,-0.6068,259.88,-0.38258,0.90832,0.16906,119.78 > view matrix models > #3,0.79023,-0.023751,0.61235,46.457,-0.073749,0.9883,0.13351,230.4,-0.60835,-0.15066,0.77924,149.93 > view matrix models > #3,0.61289,-0.017424,0.78997,47.1,-0.39139,0.8618,0.32267,251.99,-0.68642,-0.50695,0.52137,203.47 > view matrix models > #3,0.56705,-0.026808,0.82325,49.118,-0.69318,0.52434,0.49454,286.51,-0.44492,-0.85109,0.27874,223.15 > view matrix models > #3,0.60659,0.090162,0.78988,41.165,-0.77261,0.30107,0.55896,302.01,-0.18741,-0.94933,0.25229,206.06 > view matrix models > #3,0.4977,-0.13993,0.85599,59.851,-0.76607,0.39189,0.50947,300.43,-0.40674,-0.90931,0.087849,240.72 > view matrix models > #3,0.61655,0.14784,0.77331,38.202,-0.77972,0.2508,0.5737,304.41,-0.10914,-0.95668,0.2699,197.11 > view matrix models > #3,0.31191,0.30931,0.89835,46.907,-0.94422,0.20607,0.25688,353,-0.10567,-0.92837,0.35633,186.97 > view matrix models > #3,0.25419,0.16131,0.95361,56.515,-0.94326,0.25918,0.20759,354.26,-0.21367,-0.95226,0.21804,212.04 > view matrix models > #3,0.19102,0.082624,0.9781,65.302,-0.981,-0.018474,0.19314,376.3,0.034027,-0.99641,0.077525,203.27 > view matrix models > #3,0.36428,-0.46497,0.80691,97.507,-0.42671,-0.85348,-0.29916,418.2,0.82778,-0.23534,-0.50931,132.78 > view matrix models > #3,0.83082,-0.35451,0.42903,79.719,0.50878,0.17133,-0.84368,313.61,0.22559,0.91922,0.32272,44.45 > view matrix models > #3,0.64718,0.22397,0.72869,34.676,-0.42691,0.8984,0.10303,273.76,-0.63159,-0.37777,0.67704,175.63 > view matrix models > #3,0.61698,0.22207,0.755,35.335,-0.45337,0.88446,0.11034,276.56,-0.64326,-0.41038,0.64638,181.64 > view matrix models > #3,0.69087,-0.16572,0.70373,56.46,-0.22389,0.87649,0.4262,224.82,-0.68744,-0.452,0.56844,195.83 > view matrix models > #3,0.39899,-0.0097501,0.91691,56.016,-0.68251,-0.67094,0.28986,377.51,0.61236,-0.74145,-0.27435,163.14 > view matrix models > #3,0.39834,-0.06371,0.91502,59.55,-0.12187,-0.99242,-0.016046,370.04,0.9091,-0.10512,-0.40309,106.86 > view matrix models > #3,0.65042,-0.16137,0.74224,56.616,-0.21463,-0.9764,-0.024193,379.02,0.72862,-0.14357,-0.6697,151.98 > view matrix models > #3,0.61975,-0.18445,0.76281,59.149,-0.014761,-0.97456,-0.22366,377.68,0.78466,0.12735,-0.60671,124 > view matrix models > #3,0.36142,0.39819,0.8431,41.721,-0.077117,-0.88836,0.45262,315.54,0.92921,-0.2286,-0.29036,101.89 > view matrix models > #3,0.063985,-0.22245,0.97284,97.02,-0.30904,-0.93134,-0.19263,401.35,0.94889,-0.28832,-0.12834,88.473 > view matrix models > #3,0.49313,-0.46564,0.73485,91.486,-0.45569,-0.8578,-0.23776,415.61,0.74106,-0.21762,-0.63519,152.04 > view matrix models > #3,0.64355,-0.21994,0.73312,61.723,-0.2712,-0.96121,-0.050299,386.14,0.71575,-0.16645,-0.67823,155.45 > view matrix models > #3,0.40812,-0.077508,0.90963,59.924,-0.32419,-0.94375,0.065039,379.58,0.85343,-0.32144,-0.4103,126.26 > view matrix models > #3,0.35449,-0.17546,0.91845,70.403,-0.38848,-0.92109,-0.026024,393.06,0.85054,-0.34758,-0.39468,126.69 > view matrix models > #3,0.92953,-0.19655,0.312,71.196,0.19305,0.98027,0.042399,212.91,-0.31418,0.02082,0.94914,94.429 > view matrix models > #3,0.89398,-0.16992,0.41465,63.525,0.1318,0.98409,0.11911,211.6,-0.42829,-0.051832,0.90215,114.57 > view matrix models > #3,0.90191,-0.1603,0.40108,63.416,0.097932,0.98029,0.17157,210.3,-0.42068,-0.11547,0.89983,117.91 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.90191,-0.1603,0.40108,45.199,0.097932,0.98029,0.17157,98.109,-0.42068,-0.11547,0.89983,130.4 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.90462,-0.15228,0.39808,44.72,0.075784,0.97658,0.20136,97.755,-0.41942,-0.15198,0.89498,132.96 > view matrix models > #3,0.91324,0.096479,0.39584,28.888,-0.12657,0.99067,0.05056,131.03,-0.38727,-0.096276,0.91693,124.32 > view matrix models > #3,0.91314,0.10295,0.39444,28.633,-0.13416,0.98958,0.052321,131.69,-0.38494,-0.1007,0.91743,124.31 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.91314,0.10295,0.39444,38.931,-0.13416,0.98958,0.052321,137.5,-0.38494,-0.1007,0.91743,125.84 > select subtract #3 Nothing selected > hide #!3 models > select /E 3290 atoms, 3325 bonds, 4 pseudobonds, 423 residues, 3 models selected > cartoon #2 > show #2 target ab > hide #2 target a > cartoon #2 > show #!3 models > cartoon (#!3 & sel) > cartoon hide (#!3 & sel) > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > close #3 > open /Users/wkeliason/Downloads/ChimeraX/PDB/GsDnaB_Xray/4esv.pdb.gz 4esv.pdb.gz title: A new twist on the translocation mechanism of helicases from the structure of DNAb with its substrates [more info...] Chain information for 4esv.pdb.gz #3 --- Chain | Description | UniProt A B C D E F G H I J K L | DNAB | Q9X4C9_GEOSE 1-445 1-454 V | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | W | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | Non-standard residues in 4esv.pdb.gz #3 --- ALF — tetrafluoroaluminate ion CA — calcium ion GDP — guanosine-5'-diphosphate MES — 2-(N-morpholino)-ethanesulfonic acid > delete /F,G,H,I,J,K,L,W > delete /v [Repeated 1 time(s)] > select add #3 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > cartoon (#!3 & sel) > hide (#!3 & sel) target a > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 16540 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > volume #1 level 0.2654 > hide #!1 models > volume #2 level 0.08099 > view matrix models #3,1,0,0,65.58,0,1,0,7.5259,0,0,1,72.001 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.70395,-0.49414,0.51018,77.539,0.70925,0.52724,-0.46796,9.6638,-0.037747,0.69127,0.72161,59.506 > view matrix models > #3,0.67942,-0.51298,0.52464,79.775,0.7322,0.52044,-0.43935,5.1332,-0.047661,0.68264,0.7292,60.309 > view matrix models > #3,0.63903,-0.33515,0.69232,57.288,0.73768,0.522,-0.42819,3.4541,-0.21788,0.78434,0.58081,84.827 > view matrix models > #3,0.84451,-0.17702,0.50544,44.676,0.19976,0.9798,0.0093847,-11.934,-0.49689,0.09304,0.86281,128.41 > view matrix models > #3,0.5956,0.17738,0.78345,21.809,-0.65655,0.66943,0.34756,60.432,-0.46282,-0.72138,0.51517,207.17 > view matrix models > #3,0.030322,-0.20685,0.9779,83.213,-0.93797,-0.34396,-0.043672,186.7,0.34539,-0.91592,-0.20445,205.97 > view matrix models > #3,0.16586,-0.50242,0.84857,99.872,-0.94262,-0.33361,-0.013285,183.7,0.28977,-0.79767,-0.52892,234.53 > view matrix models > #3,0.66924,-0.093912,0.73709,35.389,-0.52061,-0.76706,0.37495,132.09,0.53018,-0.63467,-0.56223,203.84 > view matrix models > #3,0.70123,0.13542,0.69996,21.677,0.3901,0.7489,-0.5357,34.111,-0.59674,0.6487,0.47232,140.81 > view matrix models > #3,-0.97484,0.15632,-0.15893,266.78,0.22095,0.5828,-0.782,84.002,-0.029612,-0.79744,-0.60268,273.08 > view matrix models > #3,-0.45098,0.065232,-0.89015,288.56,0.82758,0.40405,-0.38968,-1.8569,0.33424,-0.91241,-0.2362,209.83 > view matrix models > #3,-0.59029,0.011327,-0.80711,297.93,0.73803,0.41254,-0.53397,19.966,0.32692,-0.91087,-0.25188,211.92 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.59029,0.011327,-0.80711,309.31,0.73803,0.41254,-0.53397,127.63,0.32692,-0.91087,-0.25188,215.01 > view matrix models > #3,-0.59029,0.011327,-0.80711,406.93,0.73803,0.41254,-0.53397,81.769,0.32692,-0.91087,-0.25188,237.18 > volume #2 level 0.07452 > view matrix models > #3,-0.59029,0.011327,-0.80711,398.31,0.73803,0.41254,-0.53397,83.254,0.32692,-0.91087,-0.25188,236.2 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.47596,-0.18535,0.85971,149.08,-0.28466,-0.95739,-0.048805,223.1,0.83212,-0.2215,-0.50844,167.92 > view matrix models > #3,0.64643,-0.37319,0.66548,161.75,0.50354,-0.44662,-0.73958,178.14,0.57322,0.81318,-0.1008,92.424 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.64643,-0.37319,0.66548,60.211,0.50354,-0.44662,-0.73958,204.52,0.57322,0.81318,-0.1008,94.66 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.78879,0.019271,0.61436,26.895,0.53693,-0.50814,-0.67343,198.79,0.29921,0.86106,-0.41116,147.87 > view matrix models > #3,0.90842,0.28772,0.30329,27.648,0.047112,0.6504,-0.75813,184.56,-0.41539,0.70299,0.57729,136.23 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.90842,0.28772,0.30329,33.608,0.047112,0.6504,-0.75813,204.08,-0.41539,0.70299,0.57729,128.75 > view matrix models > #3,0.90842,0.28772,0.30329,32.824,0.047112,0.6504,-0.75813,206.68,-0.41539,0.70299,0.57729,129.07 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.62608,-0.58151,0.51949,93.739,0.071494,-0.6206,-0.78086,283.97,0.77648,0.52602,-0.34697,107.83 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.62608,-0.58151,0.51949,94.457,0.071494,-0.6206,-0.78086,282.34,0.77648,0.52602,-0.34697,107.72 > view matrix models > #3,0.62608,-0.58151,0.51949,96.634,0.071494,-0.6206,-0.78086,285.08,0.77648,0.52602,-0.34697,104.75 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.93946,0.14061,0.31248,40.764,0.031465,0.87267,-0.48729,170.51,-0.34121,0.46762,0.81542,110.79 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.93946,0.14061,0.31248,41.628,0.031465,0.87267,-0.48729,173.62,-0.34121,0.46762,0.81542,112.84 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.87648,-0.033962,0.48023,42.889,0.22412,0.91161,-0.34458,138.82,-0.42608,0.40965,0.80662,125.62 > view matrix models > #3,0.78869,-0.29785,0.53782,62.338,0.61458,0.35876,-0.70256,167.22,0.016307,0.88463,0.466,84.496 > view matrix models > #3,0.90549,-0.027236,0.4235,44.892,0.044557,0.99852,-0.031051,122.09,-0.42203,0.046986,0.90537,138.15 > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > select /B 3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > select /C 3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected > volume #2 level 0.0618 > view matrix models > #3,0.13396,-0.34893,0.92753,94.07,-0.23303,-0.92081,-0.31275,293.08,0.9632,-0.17425,-0.20466,117.74 > view matrix models > #3,0.89292,0.021068,0.44973,40.744,0.027763,0.99443,-0.10171,130.6,-0.44937,0.1033,0.88735,139.1 > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > select /B 3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected > cartoon hide (#!3 & sel) > select /C 3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected > cartoon hide (#!3 & sel) > select /D 3369 atoms, 3406 bonds, 5 pseudobonds, 436 residues, 3 models selected > cartoon hide (#!3 & sel) > select /E 3290 atoms, 3325 bonds, 4 pseudobonds, 423 residues, 3 models selected > cartoon hide (#!3 & sel) > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > view matrix models > #3,0.72662,0.40274,0.55662,34.599,0.1959,0.65508,-0.72972,168.88,-0.65852,0.63927,0.3971,169.9 > view matrix models > #3,0.95188,0.17484,0.25169,38.556,0.034591,0.75474,-0.65511,178.87,-0.3045,0.6323,0.71238,105.23 > view matrix models > #3,0.97656,0.11228,0.18363,43.236,0.023622,0.79208,-0.60996,175.3,-0.21394,0.6,0.77086,91.74 > view matrix models > #3,0.97171,-0.049536,-0.23092,79.715,-0.066705,0.88038,-0.46956,172.68,0.22655,0.47168,0.85217,38.102 > view matrix models > #3,0.99099,0.13201,-0.022807,54.104,-0.092826,0.55388,-0.82741,216.58,-0.096595,0.82207,0.56114,79.512 > view matrix models > #3,0.62442,-0.48693,0.61073,89.859,0.77961,0.34054,-0.52558,98.894,0.047937,0.80432,0.59226,60.356 > view matrix models > #3,0.62682,-0.63027,0.45811,107.11,0.76344,0.37926,-0.5228,98.719,0.15576,0.67744,0.7189,45.097 > view matrix models > #3,0.84973,-0.44481,0.28301,81.327,0.50892,0.55186,-0.66065,130.64,0.13769,0.7054,0.6953,47.464 > view matrix models > #3,0.67878,-0.56332,0.4711,96.303,0.30807,0.80078,0.51366,64.899,-0.6666,-0.20353,0.71709,193.37 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.67878,-0.56332,0.4711,97.779,0.30807,0.80078,0.51366,72.361,-0.6666,-0.20353,0.71709,195.13 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.6429,-0.60672,0.46751,104.74,0.71681,0.26146,-0.64639,126.29,0.26994,0.75068,0.603,36.515 > view matrix models > #3,0.68082,-0.53968,0.49521,94.701,-0.032325,-0.69758,-0.71578,273.96,0.73174,0.47131,-0.49237,66.074 > view matrix models > #3,0.69054,-0.52587,0.4966,92.682,-0.52843,-0.83561,-0.15006,305.44,0.49387,-0.15879,-0.85491,152.42 > view matrix models > #3,0.71671,-0.62356,0.31225,106.71,-0.5753,-0.78174,-0.24066,314.49,0.39416,-0.0071565,-0.91901,161.23 > view matrix models > #3,0.81611,-0.54196,0.20062,97.493,-0.4851,-0.83112,-0.27189,307.88,0.31409,0.12457,-0.94118,165.86 > view matrix models > #3,0.87155,-0.37531,0.31549,74.328,0.12763,0.79494,0.59311,89.883,-0.4734,-0.47666,0.74074,183.64 > select /B 3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected > cartoon (#!3 & sel) > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > cartoon hide (#!3 & sel) > select add #3 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > select subtract #3 Nothing selected > select clear > ui mousemode right ""translate selected models"" > select add #3 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > view matrix models > #3,0.87155,-0.37531,0.31549,42.11,0.12763,0.79494,0.59311,134.68,-0.4734,-0.47666,0.74074,172.23 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.88341,-0.26432,0.38693,32.081,0.035206,0.86084,0.50766,150.87,-0.46727,-0.43485,0.76978,168.09 > view matrix models > #3,0.88674,-0.29358,0.35707,34.93,0.12642,0.897,0.42356,146.82,-0.44464,-0.33045,0.83252,157.73 > view matrix models > #3,0.81929,-0.1734,0.54652,23.644,0.024558,0.96291,0.2687,169.98,-0.57285,-0.20672,0.79316,172.69 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.81929,-0.1734,0.54652,14.935,0.024558,0.96291,0.2687,141.37,-0.57285,-0.20672,0.79316,189.52 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.80687,-0.17987,0.56268,15.122,0.031751,0.96434,0.26274,141.03,-0.58988,-0.19413,0.78381,191.95 > view matrix models > #3,0.15747,-0.32503,0.9325,60.701,-0.97655,0.08911,0.19597,281.57,-0.14679,-0.9415,-0.30337,251.72 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.15747,-0.32503,0.9325,54.828,-0.97655,0.08911,0.19597,291.49,-0.14679,-0.9415,-0.30337,270.28 > view matrix models > #3,0.15747,-0.32503,0.9325,72.5,-0.97655,0.08911,0.19597,279.94,-0.14679,-0.9415,-0.30337,274.97 > view matrix models > #3,0.15747,-0.32503,0.9325,98.378,-0.97655,0.08911,0.19597,280.5,-0.14679,-0.9415,-0.30337,264.25 > view matrix models > #3,0.15747,-0.32503,0.9325,51.247,-0.97655,0.08911,0.19597,292.25,-0.14679,-0.9415,-0.30337,249.77 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.58342,-0.27173,0.76537,15.928,-0.81138,-0.23677,0.53442,252.44,0.035998,-0.93279,-0.35861,233.55 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.58342,-0.27173,0.76537,51.723,-0.81138,-0.23677,0.53442,237.73,0.035998,-0.93279,-0.35861,247.74 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.81864,-0.39772,0.41431,57.868,0.35959,-0.20754,-0.90974,227.08,0.44781,0.89373,-0.026883,129.87 > view matrix models > #3,0.81724,0.018472,0.57599,34.486,-0.20938,0.9407,0.26692,164.53,-0.53691,-0.33874,0.77265,202.54 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.81724,0.018472,0.57599,28.538,-0.20938,0.9407,0.26692,183.87,-0.53691,-0.33874,0.77265,209.64 > cartoon hide (#!3 & sel) > select /C 3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected > cartoon (#!3 & sel) > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.1212,-0.56143,0.8186,79.062,-0.34029,-0.79821,-0.49706,330.97,0.93248,-0.21832,-0.28779,196.17 > view matrix models > #3,0.64865,-0.73504,-0.19741,148.27,-0.43965,-0.15014,-0.88553,359.53,0.62126,0.66119,-0.42055,207.86 > view matrix models > #3,0.91612,-0.38479,0.11251,82.198,-0.40023,-0.89407,0.20114,265.23,0.023195,-0.22929,-0.97308,344.2 > view matrix models > #3,0.98654,-0.054124,0.15428,61.392,-0.1556,-0.60051,0.78433,173.99,0.050196,-0.79778,-0.60085,320.8 > view matrix models > #3,0.98485,-0.040736,0.16856,59.596,-0.15875,-0.6029,0.78186,174.59,0.069774,-0.79677,-0.60023,319.08 > view matrix models > #3,0.869,-0.43736,0.23142,75.216,-0.48251,-0.85264,0.20046,270.79,0.10965,-0.28586,-0.95198,336.62 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.869,-0.43736,0.23142,79.462,-0.48251,-0.85264,0.20046,237.9,0.10965,-0.28586,-0.95198,315.64 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.84982,-0.47442,0.22964,82.422,-0.51728,-0.8343,0.19068,241.23,0.10113,-0.28083,-0.95442,316.45 > view matrix models > #3,0.84938,-0.51368,0.12117,95.171,-0.4249,-0.80173,-0.42034,297.09,0.31307,0.30554,-0.89924,274.34 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.84938,-0.51368,0.12117,100.72,-0.4249,-0.80173,-0.42034,308.31,0.31307,0.30554,-0.89924,267.3 > view matrix models > #3,0.84938,-0.51368,0.12117,83.829,-0.4249,-0.80173,-0.42034,310.35,0.31307,0.30554,-0.89924,262.25 > cartoon hide (#!3 & sel) > select /C 3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected > cartoon (#!3 & sel) [Repeated 1 time(s)] > select /D 3369 atoms, 3406 bonds, 5 pseudobonds, 436 residues, 3 models selected > select /C 3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected > cartoon hide (#!3 & sel) > select /D 3369 atoms, 3406 bonds, 5 pseudobonds, 436 residues, 3 models selected > cartoon (#!3 & sel) > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.8296,-0.53655,-0.15452,118.58,-0.55754,-0.78103,-0.28132,304.91,0.030258,0.31954,-0.94709,291.96 > view matrix models > #3,0.96881,-0.24466,0.039447,67.532,-0.24391,-0.91325,0.32631,214.74,-0.043809,-0.32575,-0.94444,334.53 > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models > #3,0.96881,-0.24466,0.039447,94.457,-0.24391,-0.91325,0.32631,219.87,-0.043809,-0.32575,-0.94444,341.23 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.79164,-0.58362,0.18082,112.93,-0.60815,-0.78115,0.14128,265.9,0.058792,-0.2218,-0.97332,329.63 > view matrix models > #3,0.69294,-0.56391,0.44926,89.657,-0.33601,-0.80389,-0.49078,315.85,0.63791,0.18913,-0.74653,229.23 > view matrix models > #3,0.73886,-0.52971,0.41652,87.441,-0.24974,-0.78935,-0.56085,315.47,0.62587,0.31037,-0.71552,219.9 > view matrix models > #3,0.65906,-0.67181,0.3381,111.52,-0.41179,-0.6985,-0.58525,327.48,0.62934,0.24649,-0.737,225.67 > view matrix models > #3,0.66733,-0.73385,0.12704,138.56,-0.37076,-0.47528,-0.7979,335.75,0.64591,0.48536,-0.58925,193.75 > view matrix models > #3,0.67235,-0.73042,0.12014,138.72,-0.37573,-0.47659,-0.79479,335.91,0.63779,0.48924,-0.59487,194.9 > view matrix models > #3,0.68781,-0.72359,-0.057779,157.44,-0.31113,-0.22196,-0.92408,330.74,0.65583,0.65357,-0.3778,159.08 > view matrix models > #3,0.64491,-0.76357,-0.032473,160.57,-0.28977,-0.20499,-0.93489,329.14,0.70719,0.61233,-0.35346,154.06 > view matrix models > #3,0.7787,-0.58224,0.23372,107.91,-0.070287,-0.45114,-0.88968,318.41,0.62345,0.67637,-0.39223,162.31 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.7787,-0.58224,0.23372,103.2,-0.070287,-0.45114,-0.88968,317.95,0.62345,0.67637,-0.39223,149.5 > view matrix models > #3,0.7787,-0.58224,0.23372,102.8,-0.070287,-0.45114,-0.88968,321.43,0.62345,0.67637,-0.39223,146.14 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.62476,-0.61605,0.47974,89.995,-0.61338,-0.76741,-0.18667,306.33,0.48316,-0.17764,-0.85732,260.13 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.62476,-0.61605,0.47974,92.192,-0.61338,-0.76741,-0.18667,316.7,0.48316,-0.17764,-0.85732,273.08 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.3024,-0.8011,-0.51652,245.72,0.64025,0.57216,-0.51256,168.01,0.70615,-0.1757,0.68592,75.712 > cartoon hide (#!3 & sel) > select /E 3290 atoms, 3325 bonds, 4 pseudobonds, 423 residues, 3 models selected > cartoon (#!3 & sel) > ui mousemode right ""translate selected models"" > view matrix models > #3,0.3024,-0.8011,-0.51652,255.76,0.64025,0.57216,-0.51256,131.81,0.70615,-0.1757,0.68592,77.029 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.17246,-0.68248,0.71027,126.93,-0.8021,0.32124,0.50343,186.83,-0.57175,-0.65653,-0.49201,370.69 > view matrix models > #3,0.23996,-0.68921,0.68367,123.82,-0.82843,0.22176,0.51432,197.38,-0.50609,-0.68979,-0.51775,370.11 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.23996,-0.68921,0.68367,121.13,-0.82843,0.22176,0.51432,209.21,-0.50609,-0.68979,-0.51775,371.57 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.42674,-0.58321,-0.6912,322.39,0.90019,-0.3474,-0.26264,176.44,-0.086954,-0.73429,0.67325,208.25 > view matrix models > #3,0.22001,-0.86784,0.44547,164.85,-0.84172,0.061931,0.53636,222.87,-0.49306,-0.49296,-0.71685,373.37 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.22001,-0.86784,0.44547,162.26,-0.84172,0.061931,0.53636,221.59,-0.49306,-0.49296,-0.71685,377.35 > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 4esv.pdb.gz (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 3290 atoms average map value = 0.05965, steps = 152 shifted from previous position = 20.7 rotated from previous position = 20.2 degrees atoms outside contour = 1691, contour level = 0.061802 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.18294,-0.92075,0.3446,216.99,0.70487,-0.36718,-0.60691,232.58,0.68535,0.13187,0.71618,52.955 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.18294,-0.92075,0.3446,232.52,0.70487,-0.36718,-0.60691,243.7,0.68535,0.13187,0.71618,42.599 > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 4esv.pdb.gz (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 3290 atoms average map value = 0.06099, steps = 324 shifted from previous position = 30.7 rotated from previous position = 52.4 degrees atoms outside contour = 1621, contour level = 0.061802 > cartoon hide (#!3 & sel) > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > cartoon (#!3 & sel) > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.42976,-0.1716,0.88648,188.52,-0.76437,-0.45349,-0.45835,421.43,0.48067,-0.87458,0.063726,163.53 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.42976,-0.1716,0.88648,179.52,-0.76437,-0.45349,-0.45835,373.56,0.48067,-0.87458,0.063726,195.17 > volume #2 level 0.08387 > view matrix models > #3,-0.42976,-0.1716,0.88648,176.01,-0.76437,-0.45349,-0.45835,386.53,0.48067,-0.87458,0.063726,245.26 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.42469,0.60485,0.67364,149.25,-0.81072,-0.58526,0.014384,367.79,0.40295,-0.54002,0.73892,192.83 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.42469,0.60485,0.67364,136.46,-0.81072,-0.58526,0.014384,341.23,0.40295,-0.54002,0.73892,136.85 > cartoon hide (#!3 & sel) > ui tool show AlphaFold > alphafold predict > MSELFSERIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNLERRFDEAQIPPGA Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction AlphaFold prediction finished Results in /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16 > open > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/best_model.pdb Chain information for best_model.pdb #4 --- Chain | Description A | No description available > view matrix models > #3,-0.42469,0.60485,0.67364,203.26,-0.81072,-0.58526,0.014384,409.53,0.40295,-0.54002,0.73892,207.6 > select add #4 6839 atoms, 6917 bonds, 8 pseudobonds, 880 residues, 4 models selected > select add #3 20268 atoms, 20496 bonds, 21 pseudobonds, 2610 residues, 4 models selected > select subtract #3 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models #4,1,0,0,141.3,0,1,0,149.35,0,0,1,155.44 > select subtract #4 Nothing selected > select add #4 3553 atoms, 3599 bonds, 454 residues, 1 model selected > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.86622,0.39715,0.30319,137.08,-0.47116,0.85124,0.23106,147.93,-0.16632,-0.34301,0.92449,157.46 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.86622,0.39715,0.30319,175.97,-0.47116,0.85124,0.23106,178.41,-0.16632,-0.34301,0.92449,148.23 > select subtract #4 Nothing selected > close #3 > ui mousemode right ""rotate selected models"" > select add #4 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models > #4,0.7569,0.59018,0.28069,174.62,-0.59868,0.7984,-0.064323,179.83,-0.26207,-0.11936,0.95764,146.46 > view matrix models > #4,0.68329,0.6034,-0.41113,177.7,-0.59588,0.78623,0.16359,178.81,0.42195,0.13321,0.89678,146.97 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.68329,0.6034,-0.41113,176.57,-0.59588,0.78623,0.16359,179.38,0.42195,0.13321,0.89678,140.29 > select subtract #4 Nothing selected > ui mousemode right ""rotate selected models"" > select add #4 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models > #4,0.27144,0.95624,-0.10919,171.92,-0.95029,0.28426,0.12703,181.7,0.15251,0.069281,0.98587,139.56 > select subtract #4 Nothing selected > ui mousemode right ""translate selected models"" > select add #4 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models > #4,0.27144,0.95624,-0.10919,173.31,-0.95029,0.28426,0.12703,182.49,0.15251,0.069281,0.98587,144.88 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.36509,0.91022,-0.19548,174.24,-0.91108,0.3925,0.12603,181.94,0.19144,0.13209,0.97258,144.67 > view matrix models > #4,0.49451,0.86802,-0.044869,174.1,-0.85284,0.49453,0.16764,181.27,0.1677,-0.044631,0.98483,145.62 > select subtract #4 Nothing selected > fitmap #4 inMap #2 moveWholeMolecules false Fit molecule best_model.pdb (#4) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 3553 atoms average map value = 0.06568, steps = 752 shifted from previous position = 18.2 rotated from previous position = 44.9 degrees atoms outside contour = 2624, contour level = 0.083873 > select : 181-454 2138 atoms, 2162 bonds, 274 residues, 1 model selected > view matrix models > #4,0.56866,0.81473,-0.1133,175.51,-0.75309,0.57107,0.3267,176.57,0.33088,-0.10045,0.93831,145.99 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.56866,0.81473,-0.1133,173.91,-0.75309,0.57107,0.3267,172.57,0.33088,-0.10045,0.93831,141.71 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.24758,0.50377,-0.8276,193.81,-0.53409,0.78365,0.31723,169.26,0.80836,0.36347,0.46308,143.86 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.24758,0.50377,-0.8276,177.82,-0.53409,0.78365,0.31723,172.67,0.80836,0.36347,0.46308,135.98 > fitmap sel inMap #2 moveWholeMolecules false Fit molecule best_model.pdb (#4) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 2138 atoms average map value = 0.06752, steps = 216 shifted from previous position = 2.51 rotated from previous position = 41.1 degrees atoms outside contour = 1556, contour level = 0.083873 > close #4 > open > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb Chain information for af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb #3 --- Chain | Description A | No description available Chain information for af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb #4 --- Chain | Description A | No description available Chain information for af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb #5 --- Chain | Description A | No description available Chain information for af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #6 --- Chain | Description A | No description available Chain information for af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #7 --- Chain | Description A | No description available > select add #2 2 models selected > select subtract #2 Nothing selected > select add #3 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models #3,1,0,0,154.8,0,1,0,136.78,0,0,1,74.917 > select subtract #3 Nothing selected > select add #4 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models #4,1,0,0,121.71,0,1,0,112.13,0,0,1,212.54 > select subtract #4 Nothing selected > select add #5 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models #5,1,0,0,71.136,0,1,0,66.941,0,0,1,171.15 > select subtract #5 Nothing selected > select add #6 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models #6,1,0,0,91.563,0,1,0,80.861,0,0,1,42.954 > select subtract #6 Nothing selected > select add #7 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models #7,1,0,0,55.655,0,1,0,56.71,0,0,1,278.98 > select subtract #7 Nothing selected > select add #3 3553 atoms, 3599 bonds, 454 residues, 1 model selected > select subtract #3 Nothing selected > select add #4 3553 atoms, 3599 bonds, 454 residues, 1 model selected > select subtract #4 Nothing selected > select add #5 3553 atoms, 3599 bonds, 454 residues, 1 model selected > select subtract #5 Nothing selected > select add #6 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models #6,1,0,0,177.24,0,1,0,98.919,0,0,1,161.92 > view matrix models #6,1,0,0,142.92,0,1,0,164.64,0,0,1,140.27 > view matrix models #6,1,0,0,175.1,0,1,0,164.55,0,0,1,150.54 > select : 181-454 10690 atoms, 10810 bonds, 1370 residues, 5 models selected > select add #5 12105 atoms, 12247 bonds, 1550 residues, 5 models selected > select subtract #5 8552 atoms, 8648 bonds, 1096 residues, 4 models selected > select add #4 9967 atoms, 10085 bonds, 1276 residues, 4 models selected > select subtract #4 6414 atoms, 6486 bonds, 822 residues, 3 models selected > select add #3 7829 atoms, 7923 bonds, 1002 residues, 3 models selected > select subtract #3 4276 atoms, 4324 bonds, 548 residues, 2 models selected > select add #7 5691 atoms, 5761 bonds, 728 residues, 2 models selected > select subtract #7 2138 atoms, 2162 bonds, 274 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.91502,0.14207,0.37756,172.81,-0.19726,0.97398,0.11155,162.71,-0.35189,-0.17655,0.91924,148.54 > view matrix models > #6,0.98386,-0.002578,0.17891,174.34,0.0049876,0.9999,-0.01302,164.64,-0.17886,0.013702,0.98378,149.22 > view matrix models > #6,0.81065,0.57137,-0.12802,172.96,-0.563,0.70052,-0.43853,162.49,-0.16088,0.42757,0.88955,148.85 > view matrix models > #6,0.83929,0.53608,-0.090665,173.12,-0.52084,0.74492,-0.41692,162.64,-0.15596,0.39713,0.90441,148.9 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.83929,0.53608,-0.090665,181.69,-0.52084,0.74492,-0.41692,174.18,-0.15596,0.39713,0.90441,151.56 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.84525,0.52583,-0.09519,181.77,-0.51417,0.75175,-0.41293,174.21,-0.14557,0.39797,0.90577,151.63 > view matrix models > #6,0.82652,0.55604,-0.087673,181.54,-0.54773,0.7585,-0.35308,173.72,-0.12983,0.33985,0.93147,151.78 > view matrix models > #6,0.90974,-0.023251,-0.41452,184.53,-0.068681,0.97625,-0.20549,176.37,0.40945,0.21542,0.88654,156.27 > view matrix models > #6,0.35444,-0.92362,-0.14593,181.21,-0.93037,-0.36398,0.043969,171.7,-0.093728,0.12019,-0.98832,159.41 > view matrix models > #6,0.16354,-0.98512,-0.05295,179.56,-0.98394,-0.15898,-0.081181,171.32,0.071555,0.065375,-0.99529,160.8 > view matrix models > #6,0.65346,-0.53695,-0.53355,184.08,-0.71214,-0.19712,-0.6738,175.59,0.25663,0.82026,-0.51119,158.91 > view matrix models > #6,0.34096,-0.85598,-0.38863,181.85,-0.80085,-0.047977,-0.59694,174.34,0.49233,0.51477,-0.70187,162 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.34096,-0.85598,-0.38863,177.63,-0.80085,-0.047977,-0.59694,159.07,0.49233,0.51477,-0.70187,147.06 > select add #6 3553 atoms, 3599 bonds, 454 residues, 1 model selected > select subtract #6 Nothing selected > select add #5 3553 atoms, 3599 bonds, 454 residues, 1 model selected > select subtract #5 Nothing selected > select add #4 3553 atoms, 3599 bonds, 454 residues, 1 model selected > select subtract #4 Nothing selected > select add #3 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models #3,1,0,0,119.56,0,1,0,9.4868,0,0,1,77.51 > select subtract #3 Nothing selected > select add #6 3553 atoms, 3599 bonds, 454 residues, 1 model selected > view matrix models > #6,0.34096,-0.85598,-0.38863,178.08,-0.80085,-0.047977,-0.59694,138.06,0.49233,0.51477,-0.70187,162.59 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.11441,-0.20695,-0.97164,177.14,-0.59668,0.76767,-0.23377,136.63,0.79428,0.60651,-0.035655,162.29 > view matrix models > #6,-0.051355,-0.48219,-0.87456,176.1,-0.99395,0.10979,-0.0021657,134.14,0.097061,0.86916,-0.48491,158.1 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.051355,-0.48219,-0.87456,189.87,-0.99395,0.10979,-0.0021657,183.47,0.097061,0.86916,-0.48491,150.03 > view matrix models > #6,-0.051355,-0.48219,-0.87456,178.97,-0.99395,0.10979,-0.0021657,183.9,0.097061,0.86916,-0.48491,142.53 > view matrix models > #6,-0.051355,-0.48219,-0.87456,180.06,-0.99395,0.10979,-0.0021657,182.13,0.097061,0.86916,-0.48491,140.82 > view matrix models > #6,-0.051355,-0.48219,-0.87456,176.75,-0.99395,0.10979,-0.0021657,179.41,0.097061,0.86916,-0.48491,139.55 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.09051,-0.21443,-0.97254,177.62,-0.96608,0.21824,-0.13803,179.88,0.24184,0.95205,-0.1874,139.41 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.09051,-0.21443,-0.97254,175.79,-0.96608,0.21824,-0.13803,179.73,0.24184,0.95205,-0.1874,139.72 > fitmap #6 inMap #2 moveWholeMolecules false Fit molecule af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb (#6) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 3553 atoms average map value = 0.05906, steps = 248 shifted from previous position = 13.1 rotated from previous position = 39.5 degrees atoms outside contour = 2867, contour level = 0.083873 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.057493,-0.31556,-0.94716,176.74,-0.95956,0.24441,-0.13967,179.55,0.27557,0.91689,-0.28875,138.72 > view matrix models > #6,-0.27637,-0.23646,-0.93151,176.85,-0.94173,0.26003,0.21339,183.52,0.19177,0.9362,-0.29454,138.64 > hide #7 models > select subtract #6 Nothing selected > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #!2 models > show #!2 models > open /Users/wkeliason/Downloads/output_raw.cif Summary of feedback from opening /Users/wkeliason/Downloads/output_raw.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for output_raw.cif #8 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 9 | No description available A | No description available A0 | No description available A1 | No description available A2 | No description available A3 | No description available A4 | No description available A5 | No description available A6 | No description available A8 CF | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK | No description available AL | No description available AM | No description available AN | No description available AO | No description available AP | No description available AQ | No description available AR | No description available AS | No description available AT | No description available AU | No description available AV | No description available AW | No description available AX | No description available AY | No description available AZ | No description available Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available Ai | No description available Aj | No description available Ak | No description available Al | No description available Am | No description available An | No description available Ao | No description available Ap | No description available Aq | No description available Ar | No description available As | No description available At | No description available Au | No description available Av | No description available Aw | No description available Ax | No description available Ay | No description available Az | No description available B | No description available B0 | No description available B1 | No description available B2 | No description available B7 | No description available BC DN | No description available BH | No description available BK | No description available BO | No description available BQ | No description available BT | No description available BU | No description available BW | No description available Ba | No description available Bk | No description available Bl | No description available Bn | No description available Br | No description available Bs | No description available Bw | No description available C | No description available C2 | No description available CD | No description available CG | No description available CH | No description available CI | No description available CM | No description available CN | No description available CO | No description available CQ | No description available CS | No description available CW | No description available Ca | No description available Ce DC | No description available Cp | No description available Cs | No description available Cw | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > select add #8 14223 atoms, 14113 bonds, 1763 residues, 1 model selected > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 9993 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > hide sel atoms > show sel cartoons > volume #2 level 0.07633 > volume #2 level 0.06654 > select subtract #8 Nothing selected > hide #8 models > select #8/0 27 atoms, 27 bonds, 4 residues, 1 model selected > cartoon #2 > show #7 models > hide #7 models > show #8 models > select #8/0 27 atoms, 27 bonds, 4 residues, 1 model selected > select #8/1 33 atoms, 32 bonds, 4 residues, 1 model selected > select add #8 14223 atoms, 14113 bonds, 1763 residues, 1 model selected > select subtract #8 Nothing selected > close #8 > show #7 models > select add #7 3553 atoms, 3599 bonds, 454 residues, 1 model selected > show sel cartoons [Repeated 2 time(s)] > delete :1-155 > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,152.43,0,1,0,80.28,0,0,1,187.44 > view matrix models #7,1,0,0,159.07,0,1,0,154.68,0,0,1,214.81 > view matrix models #7,1,0,0,171.43,0,1,0,185.17,0,0,1,224.39 > view matrix models #7,1,0,0,166.15,0,1,0,190.88,0,0,1,217.73 > select subtract #7 Nothing selected > select add #7 2343 atoms, 2370 bonds, 299 residues, 1 model selected > view matrix models #7,1,0,0,161.85,0,1,0,191.26,0,0,1,223.25 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.99942,0.0068874,0.033254,162.16,0.030437,0.2526,-0.96709,185.41,-0.015061,0.96755,0.25224,209.69 > view matrix models > #7,-0.53661,-0.17096,-0.82633,168.44,-0.59827,-0.6135,0.51544,211.98,-0.59508,0.77097,0.22693,215.98 > view matrix models > #7,0.907,-0.29347,0.30204,167.65,0.30553,0.95215,0.0076701,188.81,-0.28984,0.085327,0.95326,224.92 > view matrix models > #7,0.91992,-0.39162,-0.019694,164.76,0.38703,0.89877,0.20596,190.45,-0.062958,-0.19709,0.97836,224.8 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.91992,-0.39162,-0.019694,174.26,0.38703,0.89877,0.20596,210.17,-0.062958,-0.19709,0.97836,216.98 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.91592,-0.39848,-0.047943,174.04,0.21966,0.39772,0.89083,221.91,-0.33591,-0.82646,0.45181,217.82 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.91592,-0.39848,-0.047943,173.6,0.21966,0.39772,0.89083,217.47,-0.33591,-0.82646,0.45181,212.02 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.90922,-0.4163,0.0022603,174.29,0.18724,0.41379,0.89091,217.68,-0.37182,-0.80961,0.45418,212.27 > view matrix models > #7,0.99285,-0.10223,0.061702,172.23,0.00040162,0.51961,0.8544,218.38,-0.1194,-0.84827,0.51593,210.82 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.99285,-0.10223,0.061702,173.43,0.00040162,0.51961,0.8544,221.07,-0.1194,-0.84827,0.51593,207.88 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.80697,0.24993,0.53511,177.95,-0.59048,0.3232,0.73951,226.52,0.011879,-0.91273,0.40839,205.94 > view matrix models > #7,0.81773,0.25389,0.51658,177.64,-0.57559,0.36549,0.73152,226.04,-0.0030836,-0.89552,0.44501,206.35 > view matrix models > #7,0.8666,0.24178,0.43651,176.42,-0.49693,0.33865,0.79898,226.18,0.045355,-0.90932,0.41363,205.66 > view matrix models > #7,0.60088,-0.76471,-0.23273,178,0.017504,-0.2785,0.96028,226.86,-0.79915,-0.58108,-0.15396,205.54 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.60088,-0.76471,-0.23273,178.54,0.017504,-0.2785,0.96028,223.28,-0.79915,-0.58108,-0.15396,209.47 > hide #7 models > show #7 models Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as #8, grid size 113,115,103, pixel 0.667, shown at level 0.187, step 1, values float32 Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as #9, grid size 113,115,103, pixel 0.667, shown at level 0.187, step 1, values float32 > fitmap #7 inMap #2 resolution 2 moveWholeMolecules false Fit map af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian using 42152 points correlation = 0.7124, correlation about mean = 0.009181, overlap = 3491 steps = 264, shift = 21.1, angle = 28.8 degrees Position of af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 (#9) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.46276591 -0.86980490 0.17113491 189.05644106 -0.40941583 -0.03847764 0.91153616 201.96759635 -0.78627375 -0.49189320 -0.37391803 203.19240477 Axis -0.79732539 0.54392922 0.26155923 Axis point 0.00000000 240.30764452 59.52254519 Rotation angle (degrees) 118.34729718 Shift along axis 12.26342377 Average map value = 0.07022 for 2343 atoms, 973 outside contour Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as #8, grid size 103,121,117, pixel 0.667, shown at level 0.189, step 1, values float32 > view matrix models > #7,0.60088,-0.76471,-0.23273,161.53,0.017504,-0.2785,0.96028,226.51,-0.79915,-0.58108,-0.15396,201.13 > view matrix models > #7,0.60088,-0.76471,-0.23273,168.24,0.017504,-0.2785,0.96028,222.16,-0.79915,-0.58108,-0.15396,214.41 > view matrix models > #7,0.60088,-0.76471,-0.23273,159.81,0.017504,-0.2785,0.96028,215.29,-0.79915,-0.58108,-0.15396,210.9 > view matrix models > #7,0.60088,-0.76471,-0.23273,165,0.017504,-0.2785,0.96028,238.4,-0.79915,-0.58108,-0.15396,205.35 > view matrix models > #7,0.60088,-0.76471,-0.23273,169.4,0.017504,-0.2785,0.96028,238.12,-0.79915,-0.58108,-0.15396,206.92 > fitmap #7 inMap #2 resolution 2 moveWholeMolecules false Fit map af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian using 42169 points correlation = 0.7144, correlation about mean = 0.007115, overlap = 3477 steps = 224, shift = 16.8, angle = 33.8 degrees Position of af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 (#8) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.47279123 -0.84163271 0.26100354 194.78227338 -0.47935219 0.00288471 0.87761790 220.85853234 -0.73938484 -0.54004266 -0.40207461 201.01378164 Axis -0.79980477 0.56439138 0.20438862 Axis point -0.00000000 254.49891858 43.89231021 Rotation angle (degrees) 117.59374784 Shift along axis 9.94779082 Average map value = 0.07 for 2343 atoms, 988 outside contour Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as #8, grid size 101,118,129, pixel 0.667, shown at level 0.189, step 1, values float32 > view matrix models > #7,0.60088,-0.76471,-0.23273,175.55,0.017504,-0.2785,0.96028,248.33,-0.79915,-0.58108,-0.15396,197.34 > select subtract #7 Nothing selected > hide #7 models > show #6 models > ui mousemode right ""rotate selected models"" > select add #6 2343 atoms, 2370 bonds, 299 residues, 1 model selected > view matrix models > #6,-0.33064,-0.084353,-0.93998,178.51,-0.94332,-0.00078486,0.33189,183.17,-0.028733,0.99644,-0.079312,144.56 > view matrix models > #6,0.71325,-0.21129,0.66831,181.91,-0.25318,0.81144,0.52675,181.34,-0.65359,-0.54491,0.52526,149.9 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.71325,-0.21129,0.66831,172.23,-0.25318,0.81144,0.52675,181.35,-0.65359,-0.54491,0.52526,152.59 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.46751,0.088384,0.87956,180.05,0.88114,0.033262,-0.47169,149.02,-0.070946,0.99553,-0.062328,148.02 > view matrix models > #6,0.72867,-0.15612,0.66683,172.37,0.49177,0.79694,-0.35079,160.86,-0.47666,0.58353,0.65748,159.19 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.72867,-0.15612,0.66683,164.32,0.49177,0.79694,-0.35079,183.84,-0.47666,0.58353,0.65748,149.9 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.38638,0.16351,0.90773,173.94,0.02955,0.98146,-0.18937,193.29,-0.92187,0.09999,0.37438,149.53 > view matrix models > #6,0.34491,0.30842,0.88652,175.23,-0.21603,0.9452,-0.24479,195.79,-0.91344,-0.10708,0.39264,148.25 > view matrix models > #6,-0.21778,0.75653,0.61663,182.83,-0.40663,0.50402,-0.76198,189.49,-0.88726,-0.41668,0.19786,143.58 > view matrix models > #6,0.60024,0.24849,0.76024,169.86,-0.18876,0.96768,-0.16725,196.46,-0.77723,-0.043108,0.62774,149.52 > view matrix models > #6,0.60796,0.094348,0.78835,169.05,0.02922,0.98958,-0.14097,193.91,-0.79343,0.10874,0.59887,150.42 > view matrix models > #6,0.67479,0.16734,0.71879,167.81,-0.14964,0.98475,-0.08878,196.94,-0.72268,-0.04765,0.68954,149.46 > view matrix models > #6,0.66227,0.22921,0.71335,168.33,-0.23018,0.96826,-0.097426,197.84,-0.71304,-0.099673,0.694,149.03 > view matrix models > #6,0.50574,-0.12517,0.85356,169.75,-0.28329,0.91045,0.30137,202.8,-0.81484,-0.39422,0.42499,145.36 > hide #6 models > show #6 models > hide #6 models > show #6 models > view matrix models > #6,0.33406,-0.40229,0.85239,170.25,-0.60937,0.59775,0.52093,207.74,-0.71908,-0.69344,-0.045459,136.61 > view matrix models > #6,0.83581,0.10274,0.53931,163.09,0.12501,0.92091,-0.36918,189.5,-0.53459,0.37599,0.75687,150.46 > view matrix models > #6,0.7681,-0.42208,0.48153,159.86,0.52431,0.84626,-0.094562,186.69,-0.36759,0.3251,0.87131,149.15 > view matrix models > #6,0.67901,-0.68107,-0.27403,150.63,-0.13429,0.25174,-0.95843,181.8,0.72174,0.68759,0.079469,127.42 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.67901,-0.68107,-0.27403,164.99,-0.13429,0.25174,-0.95843,191.02,0.72174,0.68759,0.079469,157.78 > view matrix models > #6,0.67901,-0.68107,-0.27403,158.08,-0.13429,0.25174,-0.95843,190.6,0.72174,0.68759,0.079469,151.8 > view matrix models > #6,0.67901,-0.68107,-0.27403,156.73,-0.13429,0.25174,-0.95843,204.59,0.72174,0.68759,0.079469,149.05 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.64204,-0.66056,-0.38915,156.05,-0.076998,0.44947,-0.88997,205.91,0.76279,0.60136,0.23772,149.74 > view matrix models > #6,0.5273,-0.67905,-0.51072,156.1,0.34032,0.71955,-0.60534,205.26,0.77855,0.14539,0.61052,150.8 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.5273,-0.67905,-0.51072,158.03,0.34032,0.71955,-0.60534,198.28,0.77855,0.14539,0.61052,150.38 > volume #2 level 0.03253 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.66289,-0.71104,-0.23452,159.15,0.55438,0.67666,-0.48455,196.45,0.50322,0.19119,0.84274,157.16 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.66289,-0.71104,-0.23452,154.59,0.55438,0.67666,-0.48455,193.66,0.50322,0.19119,0.84274,155.31 > view matrix models > #6,0.66289,-0.71104,-0.23452,154.55,0.55438,0.67666,-0.48455,193.6,0.50322,0.19119,0.84274,154.83 > view matrix models > #6,0.66289,-0.71104,-0.23452,154.86,0.55438,0.67666,-0.48455,194.4,0.50322,0.19119,0.84274,160.28 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.87991,-0.34689,-0.3247,153.25,0.33984,0.93706,-0.080162,203.76,0.33207,-0.039811,0.94241,162.25 > view matrix models > #6,0.75803,-0.40097,-0.51441,152.38,0.18085,0.887,-0.42489,201.63,0.62665,0.22905,0.74488,157.7 > view matrix models > #6,0.99081,-0.066427,-0.11786,155.99,0.030732,0.9589,-0.28208,205.82,0.13176,0.27587,0.95212,167.22 > view matrix models > #6,0.96964,0.14912,0.19379,161.32,-0.16452,0.98417,0.065852,212.7,-0.18091,-0.095735,0.97883,169.36 > view matrix models > #6,0.97498,0.18985,0.11566,160.61,-0.21363,0.94406,0.2512,215.25,-0.061498,-0.26963,0.961,166.35 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.97498,0.18985,0.11566,162.07,-0.21363,0.94406,0.2512,215.02,-0.061498,-0.26963,0.961,156.24 > view matrix models > #6,0.97498,0.18985,0.11566,159.56,-0.21363,0.94406,0.2512,216.1,-0.061498,-0.26963,0.961,153.9 > view matrix models > #6,0.97498,0.18985,0.11566,160.51,-0.21363,0.94406,0.2512,215.65,-0.061498,-0.26963,0.961,156.92 Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as #9, grid size 122,99,112, pixel 0.667, shown at level 0.188, step 1, values float32 Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as #10, grid size 122,99,112, pixel 0.667, shown at level 0.188, step 1, values float32 > fitmap #6 inMap #2 resolution 2 moveWholeMolecules false Fit map af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian using 42271 points correlation = 0.7036, correlation about mean = 0.01127, overlap = 2794 steps = 144, shift = 7.4, angle = 28.3 degrees Position of af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 (#10) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.95237226 -0.29842926 0.06266634 155.62319591 0.27551743 0.93018957 0.24256449 201.71537793 -0.13067991 -0.21374603 0.96810919 160.34007064 Axis -0.60175566 0.25497374 0.75688738 Axis point -467.42126069 755.65977572 0.00000000 Rotation angle (degrees) 22.28099987 Shift along axis 79.14436176 Average map value = 0.05619 for 2343 atoms, 401 outside contour > hide #6 models > show #6 models > ui mousemode right ""rotate selected models"" Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as #9, grid size 115,102,111, pixel 0.667, shown at level 0.188, step 1, values float32 > view matrix models > #6,0.98601,0.13563,0.096872,159.5,-0.16086,0.92652,0.34011,215.79,-0.043625,-0.35094,0.93538,155.41 > view matrix models > #6,0.87993,0.38691,0.27573,165.57,0.11429,0.39093,-0.9133,193.99,-0.46116,0.83515,0.29977,169.05 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.87993,0.38691,0.27573,164.23,0.11429,0.39093,-0.9133,201.71,-0.46116,0.83515,0.29977,170.95 > hide #6 models > select subtract #6 Nothing selected > show #5 models > select add #5 2343 atoms, 2370 bonds, 299 residues, 1 model selected > view matrix models #5,1,0,0,166.55,0,1,0,114.7,0,0,1,265.84 > view matrix models #5,1,0,0,165.34,0,1,0,114.85,0,0,1,262.35 > view matrix models #5,1,0,0,219.19,0,1,0,155.58,0,0,1,273.84 > view matrix models #5,1,0,0,198.96,0,1,0,157.81,0,0,1,216.14 > view matrix models #5,1,0,0,179.29,0,1,0,216.98,0,0,1,161.09 > view matrix models #5,1,0,0,167.19,0,1,0,215.34,0,0,1,158.86 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.57409,0.77382,0.26763,185.22,0.81855,-0.53448,-0.2105,182.52,-0.019845,0.33991,-0.94025,147.94 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.57409,0.77382,0.26763,182.38,0.81855,-0.53448,-0.2105,185.36,-0.019845,0.33991,-0.94025,152.94 > view matrix models > #5,0.57409,0.77382,0.26763,183.39,0.81855,-0.53448,-0.2105,183.42,-0.019845,0.33991,-0.94025,142.8 > volume #2 level 0.07938 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.44186,0.89691,0.017905,183.81,0.23124,-0.13316,0.96374,202.98,0.86677,-0.4217,-0.26623,132.23 > view matrix models > #5,0.60308,0.75597,-0.25457,178.31,-0.32768,0.52575,0.78499,215.2,0.72727,-0.38999,0.56479,140.62 > view matrix models > #5,0.78362,-0.19766,0.58896,167.48,0.62107,0.27168,-0.73516,194.38,-0.014694,0.94187,0.33565,165.51 > hide #5 models > volume #2 level 0.07344 > show #5 models > ui mousemode right ""translate selected models"" > view matrix models > #5,0.78362,-0.19766,0.58896,146.41,0.62107,0.27168,-0.73516,267.2,-0.014694,0.94187,0.33565,189.98 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.96992,0.06731,0.23394,147.73,-0.057054,0.9971,-0.050346,288.7,-0.23665,0.035484,0.97095,179.21 > view matrix models > #5,0.48633,-0.82236,0.2953,132.82,0.45623,0.52722,0.71686,285.41,-0.74521,-0.21391,0.63159,172.81 > view matrix models > #5,0.69742,-0.61006,-0.37607,130.25,0.68172,0.40289,0.61069,281.55,-0.22104,-0.68228,0.69688,163.24 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.69742,-0.61006,-0.37607,147.39,0.68172,0.40289,0.61069,196.94,-0.22104,-0.68228,0.69688,159.02 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.71446,-0.59108,-0.37439,147.71,0.64692,0.35423,0.67529,196.7,-0.26653,-0.72467,0.63546,157.79 > view matrix models > #5,0.6798,-0.70324,-0.20817,147.18,0.61681,0.39466,0.68102,197.58,-0.39676,-0.59135,0.70206,161.23 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.6798,-0.70324,-0.20817,156.18,0.61681,0.39466,0.68102,197.22,-0.39676,-0.59135,0.70206,162.12 > view matrix models > #5,0.6798,-0.70324,-0.20817,157.02,0.61681,0.39466,0.68102,199.73,-0.39676,-0.59135,0.70206,157.94 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.71951,-0.66469,-0.20123,157.7,0.58082,0.41708,0.69906,200.41,-0.38073,-0.61986,0.68616,157.22 > view matrix models > #5,0.87431,0.020849,0.48492,176.32,-0.4732,-0.18564,0.86117,193.26,0.10797,-0.9824,-0.15244,141.65 > view matrix models > #5,0.78591,0.11843,0.60689,179.47,0.14794,0.91697,-0.37052,201.35,-0.60038,0.38098,0.70314,176.74 > view matrix models > #5,0.64111,0.33857,0.68873,184.71,-0.0003113,0.89754,-0.44093,200.74,-0.76745,0.28247,0.57553,174.18 > view matrix models > #5,0.75666,0.16185,0.63346,180.6,0.081032,0.93819,-0.33651,202.22,-0.64877,0.30595,0.69678,175.4 > view matrix models > #5,0.85912,0.34491,0.37808,181.49,-0.17773,0.89387,-0.41159,201.39,-0.47992,0.28641,0.82924,175.78 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.85912,0.34491,0.37808,178.95,-0.17773,0.89387,-0.41159,209.25,-0.47992,0.28641,0.82924,170.48 > view matrix models > #5,0.85912,0.34491,0.37808,169.16,-0.17773,0.89387,-0.41159,206.67,-0.47992,0.28641,0.82924,165.79 > volume #2 level 0.06574 > view matrix models > #5,0.85912,0.34491,0.37808,169.26,-0.17773,0.89387,-0.41159,206.83,-0.47992,0.28641,0.82924,164.8 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.74319,0.33892,0.57689,171.22,-0.66897,0.36066,0.64992,207.59,0.01221,-0.86894,0.49477,138.84 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.74319,0.33892,0.57689,173.61,-0.66897,0.36066,0.64992,205.21,0.01221,-0.86894,0.49477,146.75 > view matrix models > #5,0.74319,0.33892,0.57689,177.19,-0.66897,0.36066,0.64992,204.65,0.01221,-0.86894,0.49477,148.27 > hide #5 models > show #5 models > view matrix models > #5,0.74319,0.33892,0.57689,242.82,-0.66897,0.36066,0.64992,215.78,0.01221,-0.86894,0.49477,154.91 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.88942,-0.12031,-0.44098,229.31,0.45666,-0.19198,-0.86868,188.91,0.019857,-0.974,0.22569,150.51 > view matrix models > #5,-0.91637,-0.071816,-0.39385,230.71,0.39797,-0.27029,-0.87668,187.51,-0.043491,-0.9601,0.27626,151.39 > view matrix models > #5,-0.8734,0.08532,-0.47948,232.79,0.38965,-0.46819,-0.79308,184.57,-0.29215,-0.8795,0.37567,154.43 > view matrix models > #5,-0.65617,-0.1466,-0.74024,225.54,0.71732,-0.42573,-0.55154,186.68,-0.23429,-0.8929,0.38451,154.11 > view matrix models > #5,0.69556,0.56702,0.44123,246.02,-0.01502,0.62547,-0.78011,206.27,-0.71831,0.53599,0.44357,182.73 > view matrix models > #5,-0.56554,-0.67758,-0.47015,217.75,0.24456,-0.68222,0.68904,194.18,-0.78763,0.2747,0.55153,178.97 > view matrix models > #5,0.86781,-0.35365,-0.34905,221.21,0.084519,0.79728,-0.59766,210.87,0.48965,0.48916,0.72178,181.22 > view matrix models > #5,0.97362,-0.1677,-0.1547,226.17,0.032453,0.77294,-0.63365,210.23,0.22584,0.61192,0.75799,184.53 > view matrix models > #5,0.90662,0.096232,-0.41083,229.01,-0.32847,0.77212,-0.544,211.95,0.26486,0.62815,0.73163,184.5 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.90662,0.096232,-0.41083,160.03,-0.32847,0.77212,-0.544,216.57,0.26486,0.62815,0.73163,179.73 > view matrix models > #5,0.90662,0.096232,-0.41083,163.98,-0.32847,0.77212,-0.544,216.47,0.26486,0.62815,0.73163,161.7 > view matrix models > #5,0.90662,0.096232,-0.41083,163.5,-0.32847,0.77212,-0.544,215.34,0.26486,0.62815,0.73163,161.38 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.90215,0.24978,-0.35176,166.92,-0.36487,0.87682,-0.31315,219.47,0.23021,0.41086,0.88216,158.73 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.90215,0.24978,-0.35176,165.16,-0.36487,0.87682,-0.31315,215.46,0.23021,0.41086,0.88216,157.78 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.89927,0.29139,-0.3262,166.18,-0.37697,0.89455,-0.24014,216.48,0.22183,0.33892,0.91429,156.74 > view matrix models > #5,0.99108,-0.078858,-0.10747,160.94,0.051066,0.96934,-0.24036,216.77,0.12313,0.23272,0.96472,155.45 > view matrix models > #5,0.99917,0.040015,0.0069341,164.18,-0.040003,0.9992,-0.0018819,219.7,-0.0070039,0.001603,0.99997,151.76 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.99917,0.040015,0.0069341,161.55,-0.040003,0.9992,-0.0018819,220.37,-0.0070039,0.001603,0.99997,158.49 > view matrix models > #5,0.99917,0.040015,0.0069341,161.48,-0.040003,0.9992,-0.0018819,217.64,-0.0070039,0.001603,0.99997,157.91 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.96287,0.26576,0.047407,166.18,0.14849,-0.37475,-0.91516,183.18,-0.22544,0.88822,-0.4003,162.6 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.96287,0.26576,0.047407,164.19,0.14849,-0.37475,-0.91516,198.54,-0.22544,0.88822,-0.4003,162.37 > hide #5 models > select subtract #5 Nothing selected > close #3 > close #4 > close #5 > close #6 > close #7 > close #8 > close #9 > open /Users/wkeliason/Downloads/ChimeraX/PDB/GsDnaB_Xray/4esv.pdb.gz 4esv.pdb.gz title: A new twist on the translocation mechanism of helicases from the structure of DNAb with its substrates [more info...] Chain information for 4esv.pdb.gz #3 --- Chain | Description | UniProt A B C D E F G H I J K L | DNAB | Q9X4C9_GEOSE 1-445 1-454 V | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | W | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | Non-standard residues in 4esv.pdb.gz #3 --- ALF — tetrafluoroaluminate ion CA — calcium ion GDP — guanosine-5'-diphosphate MES — 2-(N-morpholino)-ethanesulfonic acid > hide #2-3 target a > cartoon #2-3 > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 39891 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > delete /F,G,H,I,J,K,L,W > delete /v > select add #3 16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected > view matrix models #3,1,0,0,-21.857,0,1,0,120.05,0,0,1,64.361 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.82271,0.064653,0.56478,-60.805,0.006114,0.99245,-0.12252,131.33,-0.56843,0.10425,0.8161,131.8 > ui mousemode right ""translate selected models"" > volume #2 level 0.0452 > view matrix models > #3,0.82271,0.064653,0.56478,18.813,0.006114,0.99245,-0.12252,109.69,-0.56843,0.10425,0.8161,153.26 > view matrix models > #3,0.82271,0.064653,0.56478,21.485,0.006114,0.99245,-0.12252,133.93,-0.56843,0.10425,0.8161,152.28 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.81312,0.10619,0.57233,19.217,-0.10483,0.99386,-0.035467,136.77,-0.57258,-0.031161,0.81925,160.61 > view matrix models > #3,0.8356,0.098814,0.54038,20.406,0.061782,0.96054,-0.27118,144.19,-0.54585,0.25998,0.79653,142.41 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.8356,0.098814,0.54038,23.069,0.061782,0.96054,-0.27118,156.71,-0.54585,0.25998,0.79653,146.65 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.83231,-0.041817,0.55273,30.77,0.15851,0.97347,-0.16504,136.4,-0.53116,0.22498,0.81686,145.41 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.83231,-0.041817,0.55273,34.025,0.15851,0.97347,-0.16504,128.56,-0.53116,0.22498,0.81686,145.01 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.69965,-0.12603,0.70328,38.297,0.26126,0.96128,-0.087656,111.85,-0.66501,0.24507,0.70548,167.51 > hide #!3 models > show #!3 models > view matrix models > #3,0.7681,-0.232,0.59682,47.837,0.60092,0.58308,-0.54672,143.78,-0.22115,0.77858,0.58728,101.99 > view matrix models > #3,0.86189,-0.30951,0.40168,61.399,0.50699,0.5102,-0.69473,171.35,0.01009,0.80243,0.59666,76.644 > view matrix models > #3,0.93347,0.082778,0.34897,35.405,-0.034936,0.98936,-0.14123,144.64,-0.35695,0.11964,0.92643,123.83 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.93347,0.082778,0.34897,36.86,-0.034936,0.98936,-0.14123,147.35,-0.35695,0.11964,0.92643,119.39 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.91542,0.10681,0.38808,33.553,-0.040219,0.9836,-0.17585,151.45,-0.4005,0.14537,0.90469,124.2 > view matrix models > #3,-0.1062,-0.54062,0.83454,132.89,-0.34072,-0.76869,-0.54132,321.7,0.93415,-0.34183,-0.10257,114.79 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.1062,-0.54062,0.83454,124.38,-0.34072,-0.76869,-0.54132,308.35,0.93415,-0.34183,-0.10257,120.52 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.049023,-0.64077,0.76617,131.13,0.19418,-0.75857,-0.62199,262,0.97974,0.11828,0.16161,63.445 > view matrix models > #3,0.24948,-0.38479,0.88865,74.464,0.20436,-0.87608,-0.43672,250.83,0.94657,0.29056,-0.13993,84.43 > view matrix models > #3,0.21783,-0.41673,0.88254,80.121,0.20002,-0.866,-0.45829,252.66,0.95527,0.27636,-0.10529,81.194 > view matrix models > #3,0.46824,-0.38401,0.79579,61.294,0.87419,0.33242,-0.35396,103.14,-0.12861,0.86141,0.49135,97.999 > view matrix models > #3,0.23561,-0.20948,0.949,59.587,0.93788,-0.20691,-0.27852,122.46,0.2547,0.95567,0.14772,86.169 > view matrix models > #3,0.46907,0.022913,0.88286,28.419,0.87406,-0.15514,-0.46037,142.64,0.12642,0.98763,-0.0928,119.44 > view matrix models > #3,0.24606,-0.10051,0.96403,50.538,0.91366,0.35607,-0.19607,83.047,-0.32355,0.92904,0.17945,142.41 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.24606,-0.10051,0.96403,50.207,0.91366,0.35607,-0.19607,83.37,-0.32355,0.92904,0.17945,141.84 > select /A 3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.40644,0.022826,0.91339,31.482,0.81602,0.44062,-0.37412,104.57,-0.41099,0.89741,0.16046,154.24 > view matrix models > #3,0.4841,-0.20273,0.8512,43.224,0.7873,0.52544,-0.32262,97.489,-0.38185,0.82633,0.41397,132 > view matrix models > #3,-0.29045,-0.078983,0.95363,103.3,-0.93173,-0.20368,-0.30065,310.82,0.21798,-0.97585,-0.014433,221.49 > view matrix models > #3,-0.072914,-0.025465,0.99701,74.343,-0.91505,-0.39593,-0.077032,299.96,0.39671,-0.91793,0.0055665,198.32 > view matrix models > #3,-0.074872,-0.053808,0.99574,76.375,-0.92308,-0.37403,-0.08962,300.6,0.37725,-0.92586,-0.021665,203.27 > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.074872,-0.053808,0.99574,77.775,-0.92308,-0.37403,-0.08962,306.92,0.37725,-0.92586,-0.021665,194.13 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.60598,-0.29188,0.74,48.267,0.58037,0.79841,-0.16034,92.725,-0.54402,0.52664,0.65322,134.85 > view matrix models > #3,0.57253,-0.20289,0.79438,41.13,0.72304,0.58176,-0.37252,111.44,-0.38656,0.78765,0.47977,119.53 > view matrix models > #3,0.56543,-0.1057,0.81799,33.741,0.76327,0.44292,-0.47037,124.98,-0.31259,0.89031,0.33112,119.81 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.56543,-0.1057,0.81799,37.289,0.76327,0.44292,-0.47037,120,-0.31259,0.89031,0.33112,123.78 > hide #!3 models > show #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.59963,-0.018023,0.80008,30.24,0.074411,0.99667,-0.033317,114.26,-0.79681,0.079512,0.59897,196.17 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.59963,-0.018023,0.80008,31.382,0.074411,0.99667,-0.033317,121.38,-0.79681,0.079512,0.59897,198.88 Opened 4esv.pdb.gz map 2 as #4, grid size 214,239,209, pixel 0.667, shown at level 0.188, step 1, values float32 Opened 4esv.pdb.gz map 2 as #5, grid size 214,239,209, pixel 0.667, shown at level 0.188, step 1, values float32 > fitmap #3 inMap #2 resolution 2 moveWholeMolecules false Fit map 4esv.pdb.gz map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA- DNA-Hybrid (1).mrc gaussian using 301658 points correlation = 0.6583, correlation about mean = 0.003665, overlap = 1.85e+04 steps = 136, shift = 2.56, angle = 17 degrees Position of 4esv.pdb.gz map 2 (#5) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.77480920 -0.10103496 0.62406945 35.15086863 0.08124071 0.99487463 0.06020336 108.93106154 -0.62695350 0.00405373 0.77904616 163.94598936 Axis -0.04437027 0.98857707 0.14403697 Axis point 226.04459407 0.00000000 16.01686672 Rotation angle (degrees) 39.25250559 Shift along axis 129.74137989 Average map value = 0.05204 for 16715 atoms, 6877 outside contour > delete :1-152 > volume #2 level 0.06879 > select 11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 11 models selected > select subtract #1 11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 9 models selected > select subtract #2 11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 7 models selected > select add #2 11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 9 models selected > select add #1 11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 11 models selected > select clear > select /B 2218 atoms, 2239 bonds, 2 pseudobonds, 285 residues, 2 models selected > select clear > select /C 2300 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected > select clear > select /D 2253 atoms, 2273 bonds, 5 pseudobonds, 291 residues, 3 models selected > select /E 2232 atoms, 2253 bonds, 3 pseudobonds, 286 residues, 3 models selected > delete :157-178 > delete :153-157 > delete :178-183 > volume #2 level 0.07858 Opened 4esv.pdb.gz map 2 as #4, grid size 182,190,152, pixel 0.667, shown at level 0.187, step 1, values float32 > view matrix models > #3,0.59963,-0.018023,0.80008,31.429,0.074411,0.99667,-0.033317,122.2,-0.79681,0.079512,0.59897,201.72 Opened 4esv.pdb.gz map 2 as #5, grid size 86,96,141, pixel 0.667, shown at level 0.189, step 1, values float32 > fitmap sel inMap #2 resolution 2 moveWholeMolecules false Fit map 4esv.pdb.gz map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA- DNA-Hybrid (1).mrc gaussian using 37227 points correlation = 0.7194, correlation about mean = 0.01547, overlap = 3322 steps = 252, shift = 7.8, angle = 43.7 degrees Position of 4esv.pdb.gz map 2 (#5) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.79085760 0.50961653 0.33887356 36.67591428 -0.35727074 0.83401602 -0.42044609 212.82024234 -0.49689226 0.21144338 0.84165897 137.42677989 Axis 0.46466451 0.61458647 -0.63747185 Axis point 419.92533661 155.28597730 0.00000000 Rotation angle (degrees) 42.83907883 Shift along axis 60.23273336 Average map value = 0.07556 for 2059 atoms, 1050 outside contour Opened 4esv.pdb.gz map 2 as #5, grid size 121,124,95, pixel 0.667, shown at level 0.187, step 1, values float32 Opened 4esv.pdb.gz map 2 as #5, grid size 86,96,141, pixel 0.667, shown at level 0.189, step 1, values float32 > select /A/B/C/D/E 10194 atoms, 10287 bonds, 14 pseudobonds, 1311 residues, 3 models selected > fitmap sel inMap #2 resolution 2 moveWholeMolecules false Fit map 4esv.pdb.gz map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA- DNA-Hybrid (1).mrc gaussian using 184188 points correlation = 0.6947, correlation about mean = 0.004128, overlap = 1.381e+04 steps = 68, shift = 3.95, angle = 4.64 degrees Position of 4esv.pdb.gz map 2 (#4) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) coordinates: Matrix rotation and translation 0.54545031 0.02202850 0.83785365 32.74804945 0.00804917 0.99947080 -0.03151776 130.93536904 -0.83810453 0.02393540 0.54498434 212.58828413 Axis 0.03306819 0.99941833 -0.00833625 Axis point 211.17896610 0.00000000 80.62001107 Rotation angle (degrees) 56.97856800 Shift along axis 130.16993852 Average map value = 0.06353 for 10194 atoms, 7020 outside contour > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > select subtract #3 Nothing selected > open > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb > /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb Chain information for af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #6 --- Chain | Description A | No description available Chain information for af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb #7 --- Chain | Description A | No description available Chain information for af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb #8 --- Chain | Description A | No description available Chain information for af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb #9 --- Chain | Description A | No description available Chain information for af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #10 --- Chain | Description A | No description available > select add #10 3553 atoms, 3599 bonds, 454 residues, 1 model selected > select add #9 7106 atoms, 7198 bonds, 908 residues, 2 models selected > select add #8 10659 atoms, 10797 bonds, 1362 residues, 3 models selected > select add #7 14212 atoms, 14396 bonds, 1816 residues, 4 models selected > select add #6 17765 atoms, 17995 bonds, 2270 residues, 5 models selected Opened map 2 as #11, grid size 152,170,161, pixel 0.667, shown at level 0.326, step 1, values float32 > view matrix models > #6,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9,#7,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9,#8,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9,#9,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9,#10,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9 > select clear > select add #6 3553 atoms, 3599 bonds, 454 residues, 1 model selected Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as #12, grid size 147,115,155, pixel 0.667, shown at level 0.188, step 1, values float32 > view matrix models #6,1,0,0,228.47,0,1,0,37.301,0,0,1,299.34 > select add #7 7106 atoms, 7198 bonds, 908 residues, 2 models selected > select subtract #6 3553 atoms, 3599 bonds, 454 residues, 1 model selected Opened af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb map 2 as #13, grid size 152,109,136, pixel 0.667, shown at level 0.188, step 1, values float32 > view matrix models #7,1,0,0,129.49,0,1,0,14.701,0,0,1,280.78 > select subtract #7 Nothing selected > select add #8 3553 atoms, 3599 bonds, 454 residues, 1 model selected Opened af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb map 2 as #14, grid size 116,109,161, pixel 0.667, shown at level 0.189, step 1, values float32 > view matrix models #8,1,0,0,7.2032,0,1,0,76.39,0,0,1,225.52 > select subtract #8 Nothing selected > select add #9 3553 atoms, 3599 bonds, 454 residues, 1 model selected Opened af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb map 2 as #15, grid size 141,170,128, pixel 0.667, shown at level 0.188, step 1, values float32 > view matrix models #9,1,0,0,15.004,0,1,0,174.12,0,0,1,192.37 > select subtract #9 Nothing selected > select add #10 3553 atoms, 3599 bonds, 454 residues, 1 model selected Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as #16, grid size 138,116,153, pixel 0.667, shown at level 0.187, step 1, values float32 > view matrix models #10,1,0,0,118.46,0,1,0,104.22,0,0,1,245.51 > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > select add #9 7106 atoms, 7198 bonds, 908 residues, 2 models selected > select add #8 10659 atoms, 10797 bonds, 1362 residues, 3 models selected > select add #7 14212 atoms, 14396 bonds, 1816 residues, 4 models selected > select add #6 17765 atoms, 17995 bonds, 2270 residues, 5 models selected > delete :1-180 Opened map 2 as #11, grid size 450,330,258, pixel 0.667, shown at level 0.188, step 1, values float32 > view matrix models > #6,1,0,0,274.66,0,1,0,82.566,0,0,1,221.71,#7,1,0,0,175.67,0,1,0,59.965,0,0,1,203.15,#8,1,0,0,53.388,0,1,0,121.65,0,0,1,147.89,#9,1,0,0,61.189,0,1,0,219.39,0,0,1,114.73,#10,1,0,0,164.64,0,1,0,149.49,0,0,1,167.87 > select clear > select add #6 2138 atoms, 2162 bonds, 274 residues, 1 model selected > select add #7 4276 atoms, 4324 bonds, 548 residues, 2 models selected > select add #8 6414 atoms, 6486 bonds, 822 residues, 3 models selected > select add #9 8552 atoms, 8648 bonds, 1096 residues, 4 models selected > select add #10 10690 atoms, 10810 bonds, 1370 residues, 5 models selected > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > select clear > select add #7 2138 atoms, 2162 bonds, 274 residues, 1 model selected > select subtract #7 Nothing selected > select add #7 2138 atoms, 2162 bonds, 274 residues, 1 model selected > select subtract #7 Nothing selected > select add #10 2138 atoms, 2162 bonds, 274 residues, 1 model selected Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as #16, grid size 96,96,116, pixel 0.667, shown at level 0.188, step 1, values float32 > view matrix models #10,1,0,0,169.46,0,1,0,147.75,0,0,1,170.66 > select subtract #10 Nothing selected > select add #10 2138 atoms, 2162 bonds, 274 residues, 1 model selected > view matrix models #10,1,0,0,147.2,0,1,0,155.45,0,0,1,203.07 > view matrix models #10,1,0,0,171.5,0,1,0,154.37,0,0,1,206.05 > view matrix models #10,1,0,0,166.67,0,1,0,163.25,0,0,1,286.63 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.24064,-0.79839,0.55196,173.17,0.95598,0.096584,-0.27708,151.06,0.16791,0.59434,0.78649,286.07 > view matrix models > #10,-0.34288,-0.28295,0.89575,182.1,-0.00014944,-0.95354,-0.30126,152.27,0.93938,-0.10343,0.32691,274.14 > view matrix models > #10,0.42131,0.48592,0.76575,179.43,0.88887,-0.053656,-0.45501,149.17,-0.18001,0.87235,-0.45453,277.65 > view matrix models > #10,0.71579,0.47264,0.51407,175.22,0.63069,-0.12151,-0.76646,147.52,-0.29979,0.87284,-0.38506,279.04 > view matrix models > #10,0.83106,0.39493,0.39162,173.04,0.51108,-0.26452,-0.81782,147.17,-0.21939,0.87981,-0.42167,278.23 > view matrix models > #10,0.61951,0.78449,-0.027948,171.99,0.58226,-0.4831,-0.65391,147.37,-0.52649,0.38883,-0.75606,274.9 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.61951,0.78449,-0.027948,165.03,0.58226,-0.4831,-0.65391,145.03,-0.52649,0.38883,-0.75606,208.29 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.49752,0.86739,-0.010434,166.28,0.63357,-0.37157,-0.67862,144.95,-0.5925,0.33102,-0.73442,208.65 > view matrix models > #10,0.53183,0.84678,-0.010923,165.98,0.4143,-0.27141,-0.86873,144.91,-0.73859,0.45749,-0.49516,212.32 > view matrix models > #10,0.52608,0.85038,-0.0099709,166.04,0.45475,-0.2912,-0.84167,144.84,-0.71864,0.43825,-0.5399,211.7 > view matrix models > #10,0.68965,0.62489,-0.36592,160.75,0.19969,-0.64983,-0.73338,145.91,-0.69606,0.43271,-0.57294,211.23 > view matrix models > #10,0.71141,0.59693,-0.37091,160.46,-0.0094234,-0.51963,-0.85434,146.59,-0.70272,0.61128,-0.36404,213.98 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.71141,0.59693,-0.37091,160.78,-0.0094234,-0.51963,-0.85434,144.61,-0.70272,0.61128,-0.36404,212.57 > view matrix models > #10,0.71141,0.59693,-0.37091,166.06,-0.0094234,-0.51963,-0.85434,144.07,-0.70272,0.61128,-0.36404,211.21 > view matrix models > #10,0.71141,0.59693,-0.37091,176.83,-0.0094234,-0.51963,-0.85434,155.78,-0.70272,0.61128,-0.36404,268.53 > view matrix models > #10,0.71141,0.59693,-0.37091,166.74,-0.0094234,-0.51963,-0.85434,143.02,-0.70272,0.61128,-0.36404,211.77 > view matrix models > #10,0.71141,0.59693,-0.37091,165.54,-0.0094234,-0.51963,-0.85434,144.39,-0.70272,0.61128,-0.36404,209.94 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.52426,0.67718,-0.51631,165.64,-0.019432,-0.59665,-0.80227,144.63,-0.85133,0.43063,-0.29964,210.69 > view matrix models > #10,0.5794,0.65727,-0.48196,165.55,-0.027927,-0.57498,-0.81769,144.62,-0.81457,0.48723,-0.31478,210.56 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.5794,0.65727,-0.48196,169.44,-0.027927,-0.57498,-0.81769,143.96,-0.81457,0.48723,-0.31478,209.61 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/fitgui.py"", line 651, in _undo position_history.undo() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 41, in undo if restore_position(ps): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 93, in restore_position atoms.coords = xyz File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 16715 does not match objects array length 10194 ValueError: Values array length 16715 does not match objects array length 10194 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' See log for complete Python traceback. > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.51249,0.69858,-0.49934,169.86,-0.064745,-0.54842,-0.83369,144.14,-0.85625,0.45959,-0.23583,210.49 > view matrix models > #10,-0.89541,-0.40652,0.18163,180.23,-0.11567,0.6063,0.78678,164.53,-0.42996,0.68348,-0.58991,205.49 > view matrix models > #10,0.63739,0.73039,0.24548,176.25,0.43052,-0.073356,-0.89959,142.49,-0.63905,0.67908,-0.36121,208.9 > view matrix models > #10,0.79674,0.48357,-0.36245,168.52,-0.054831,-0.53945,-0.84023,144.06,-0.60183,0.68932,-0.40328,208.32 > view matrix models > #10,0.83568,0.36587,-0.4096,167.35,-0.14147,-0.57723,-0.80423,144.77,-0.53068,0.73003,-0.43062,207.8 > view matrix models > #10,0.72296,0.44347,-0.52977,167.23,-0.11282,-0.68073,-0.7238,144.92,-0.68161,0.58304,-0.44211,208 > view matrix models > #10,0.61725,0.60103,-0.5077,168.73,-0.14792,-0.54514,-0.82519,144.74,-0.77273,0.58445,-0.24758,210.39 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.61725,0.60103,-0.5077,170.15,-0.14792,-0.54514,-0.82519,145.76,-0.77273,0.58445,-0.24758,210.44 > volume #2 level 0.08991 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/fitgui.py"", line 651, in _undo position_history.undo() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 41, in undo if restore_position(ps): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 93, in restore_position atoms.coords = xyz File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 16715 does not match objects array length 10194 ValueError: Values array length 16715 does not match objects array length 10194 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' See log for complete Python traceback. > view matrix models > #10,0.61725,0.60103,-0.5077,239.51,-0.14792,-0.54514,-0.82519,138.03,-0.77273,0.58445,-0.24758,312.12 > select subtract #10 Nothing selected > select add #9 2138 atoms, 2162 bonds, 274 residues, 1 model selected > select subtract #9 Nothing selected > select add #8 2138 atoms, 2162 bonds, 274 residues, 1 model selected > view matrix models #8,1,0,0,114.98,0,1,0,97.71,0,0,1,282.28 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.8632,0.50431,-0.023504,116.94,0.16352,-0.32332,-0.93206,81.51,-0.47765,0.80071,-0.36155,270.66 > view matrix models > #8,0.87482,0.46717,-0.1282,115.6,0.043044,-0.33854,-0.93997,81.393,-0.48253,0.81679,-0.31627,271.24 > view matrix models > #8,-0.52837,-0.00094745,-0.84901,105.94,0.82983,-0.21194,-0.5162,86.44,-0.17945,-0.97728,0.11277,268.18 > view matrix models > #8,-0.20079,0.35755,-0.91205,106.69,0.94101,0.32925,-0.078093,93.648,0.27238,-0.87393,-0.40257,262.73 > view matrix models > #8,-0.56911,0.29706,-0.76673,108.17,0.64976,0.73391,-0.19794,94.147,0.50391,-0.61084,-0.6107,261.47 > view matrix models > #8,-0.51081,-0.19753,-0.8367,105.23,0.85151,0.017726,-0.52403,87.339,0.11834,-0.98014,0.15914,268.6 > view matrix models > #8,-0.56839,-0.36343,-0.73814,105.63,0.81815,-0.15483,-0.55377,86.27,0.086975,-0.91866,0.38535,271.4 > view matrix models > #8,-0.30779,-0.8274,-0.46977,106.54,0.71484,0.12474,-0.68807,86.009,0.6279,-0.54759,0.55306,274.72 > view matrix models > #8,-0.19233,-0.77457,-0.60254,105.25,0.74686,0.28275,-0.60187,87.647,0.63656,-0.56577,0.52412,274.31 > view matrix models > #8,0.75132,0.60059,-0.27352,114.59,-0.64703,0.5888,-0.48442,90.711,-0.12989,0.54093,0.83098,282.77 > view matrix models > #8,0.23147,0.6413,-0.73154,109.8,-0.97074,0.20165,-0.13039,93.094,0.063899,0.74032,0.66921,281.76 > view matrix models > #8,0.40229,0.33563,-0.85178,107.09,-0.88117,-0.11049,-0.4597,88.033,-0.2484,0.93549,0.2513,278.03 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.40229,0.33563,-0.85178,174.37,-0.88117,-0.11049,-0.4597,145.57,-0.2484,0.93549,0.2513,208.32 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.60913,0.20294,-0.76667,174.68,-0.77548,-0.050072,-0.62938,143.9,-0.16612,0.97791,0.12688,207.09 > view matrix models > #8,0.59908,0.53874,-0.59234,178.09,-0.72165,0.042786,-0.69094,143.6,-0.34689,0.84138,0.41441,209.77 > view matrix models > #8,0.61856,0.59836,-0.50926,179.27,-0.36711,-0.35296,-0.86061,139.88,-0.6947,0.7193,0.0013312,204.72 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.61856,0.59836,-0.50926,175.41,-0.36711,-0.35296,-0.86061,142.84,-0.6947,0.7193,0.0013312,205.33 > view matrix models > #8,0.61856,0.59836,-0.50926,173.14,-0.36711,-0.35296,-0.86061,145.7,-0.6947,0.7193,0.0013312,211.65 > view matrix models > #8,0.61856,0.59836,-0.50926,171.63,-0.36711,-0.35296,-0.86061,144.06,-0.6947,0.7193,0.0013312,211.98 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.24048,-0.75476,-0.61034,164.76,0.80183,0.50883,-0.31331,153.55,0.54703,-0.41404,0.72755,214.82 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.24048,-0.75476,-0.61034,172.44,0.80183,0.50883,-0.31331,141.47,0.54703,-0.41404,0.72755,213.93 > view matrix models > #8,0.24048,-0.75476,-0.61034,171.4,0.80183,0.50883,-0.31331,141.93,0.54703,-0.41404,0.72755,206.28 > view matrix models > #8,0.24048,-0.75476,-0.61034,169.82,0.80183,0.50883,-0.31331,142.38,0.54703,-0.41404,0.72755,204.61 > fitmap #8 inMap #2 moveWholeMolecules false Fit molecule af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb (#8) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2) using 2138 atoms average map value = 0.07129, steps = 236 shifted from previous position = 10 rotated from previous position = 25.1 degrees atoms outside contour = 1624, contour level = 0.089914 > close #3 > close #4 > close #5 > close #6 > close #7 > close #8 > close #9 > close #10 > close #11 > close #12 > close #13 > close #14 > close #15 > close #16 > open /Users/wkeliason/Downloads/output_raw.cif Summary of feedback from opening /Users/wkeliason/Downloads/output_raw.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for output_raw.cif #3 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 9 | No description available A | No description available A0 | No description available A1 | No description available A2 | No description available A3 | No description available A4 | No description available A5 | No description available A6 | No description available A8 CF | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK | No description available AL | No description available AM | No description available AN | No description available AO | No description available AP | No description available AQ | No description available AR | No description available AS | No description available AT | No description available AU | No description available AV | No description available AW | No description available AX | No description available AY | No description available AZ | No description available Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available Ai | No description available Aj | No description available Ak | No description available Al | No description available Am | No description available An | No description available Ao | No description available Ap | No description available Aq | No description available Ar | No description available As | No description available At | No description available Au | No description available Av | No description available Aw | No description available Ax | No description available Ay | No description available Az | No description available B | No description available B0 | No description available B1 | No description available B2 | No description available B7 | No description available BC DN | No description available BH | No description available BK | No description available BO | No description available BQ | No description available BT | No description available BU | No description available BW | No description available Ba | No description available Bk | No description available Bl | No description available Bn | No description available Br | No description available Bs | No description available Bw | No description available C | No description available C2 | No description available CD | No description available CG | No description available CH | No description available CI | No description available CM | No description available CN | No description available CO | No description available CQ | No description available CS | No description available CW | No description available Ca | No description available Ce DC | No description available Cp | No description available Cs | No description available Cw | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > hide surfaces > hide atoms > show surfaces > hide surfaces > show cartoons > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 9993 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > select add #3 14223 atoms, 14113 bonds, 1763 residues, 1 model selected > select subtract #3 160 models selected > select /0 27 atoms, 27 bonds, 4 residues, 1 model selected > select clear > volume #2 level 0.08401 > close #3 > ui tool show AlphaFold > volume #2 level 0.0797 > ui tool show AlphaFold > fetch 2R6D Unknown command: fetch 2R6D > fetch: 2R6D Unknown command: fetch: 2R6D > ui tool show AlphaFold No sequence chosen for AlphaFold match [Repeated 1 time(s)] > alphafold match 2R6D Missing or invalid ""sequences"" argument: Sequences argument ""2R6D"" is not a chain specifier, alignment id, UniProt id, or sequence characters > alphafold match 2R6D Missing or invalid ""sequences"" argument: Sequences argument ""2R6D"" is not a chain specifier, alignment id, UniProt id, or sequence characters > help help:user > fetch 2R6D Unknown command: fetch 2R6D > fetch Unknown command: fetch > oped 2r6d Unknown command: oped 2r6d > oped: 2r6d Unknown command: oped: 2r6d > open /Users/wkeliason/Downloads/2r6d.cif.gz File reader requires uncompressed file; '/Users/wkeliason/Downloads/2r6d.cif.gz' is compressed > open /Users/wkeliason/Downloads/2r6d.pdb 2r6d.pdb title: Crystal form B1 [more info...] Chain information for 2r6d.pdb #3 --- Chain | Description | UniProt A B C D E F | DNAB helicase | Q9X4C9_BACST 1-454 > hide atoms > show cartoons > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 18085 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > select add #3 18085 atoms, 18282 bonds, 26 pseudobonds, 2340 residues, 2 models selected > view matrix models #3,1,0,0,66.035,0,1,0,151.38,0,0,1,130.42 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.91245,0.2309,-0.33782,61.275,-0.27249,0.95877,-0.080694,164.77,0.30526,0.16568,0.93775,110.98 > view matrix models > #3,0.6363,0.74904,0.18457,81.201,-0.76306,0.64628,0.0078503,196.28,-0.1134,-0.14583,0.98279,137.73 > view matrix models > #3,0.76677,0.3309,0.55006,86.261,-0.49612,0.84925,0.18069,183.32,-0.40735,-0.41144,0.81534,152.93 > view matrix models > #3,0.767,0.33202,0.54906,86.216,-0.50014,0.84541,0.18744,183.72,-0.40195,-0.41837,0.81449,152.7 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.767,0.33202,0.54906,80.202,-0.50014,0.84541,0.18744,229.58,-0.40195,-0.41837,0.81449,217.96 > color #3 #fffb00ff > view matrix models > #3,0.767,0.33202,0.54906,123.12,-0.50014,0.84541,0.18744,238.47,-0.40195,-0.41837,0.81449,218.15 > view matrix models > #3,0.767,0.33202,0.54906,134.28,-0.50014,0.84541,0.18744,204.19,-0.40195,-0.41837,0.81449,218.6 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.69733,0.37262,0.61229,138.87,-0.21263,0.92334,-0.31975,177.5,-0.68449,0.09278,0.72309,226.32 > view matrix models > #3,0.63132,0.49083,0.60043,140.88,0.67694,-0.72654,-0.11786,151.87,0.37839,0.48087,-0.79094,134 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.63132,0.49083,0.60043,141.83,0.67694,-0.72654,-0.11786,138.59,0.37839,0.48087,-0.79094,140.61 > view matrix models > #3,0.63132,0.49083,0.60043,142.38,0.67694,-0.72654,-0.11786,136.24,0.37839,0.48087,-0.79094,143.23 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.60662,0.39325,0.69092,146.63,0.79334,-0.35552,-0.49419,118.24,0.051298,0.84791,-0.52765,162.19 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.60662,0.39325,0.69092,145.46,0.79334,-0.35552,-0.49419,121.2,0.051298,0.84791,-0.52765,160.46 > cartoon hide (#!3 & sel) > select /A 3138 atoms, 3173 bonds, 4 pseudobonds, 405 residues, 2 models selected > cartoon (#!3 & sel) > select /B 2897 atoms, 2929 bonds, 4 pseudobonds, 376 residues, 2 models selected > cartoon (#!3 & sel) > view matrix models > #3,0.60662,0.39325,0.69092,144.02,0.79334,-0.35552,-0.49419,126.76,0.051298,0.84791,-0.52765,163.54 > select add #3 18085 atoms, 18282 bonds, 26 pseudobonds, 2340 residues, 2 models selected > view matrix models > #3,0.60662,0.39325,0.69092,153.95,0.79334,-0.35552,-0.49419,126.03,0.051298,0.84791,-0.52765,161.11 > select subtract #3 Nothing selected > ui mousemode right ""rotate selected models"" > select add #3 18085 atoms, 18282 bonds, 26 pseudobonds, 2340 residues, 2 models selected > view matrix models > #3,0.61679,0.43745,0.65438,151.27,0.7842,-0.41316,-0.46295,128.61,0.067846,0.79871,-0.59789,157.99 > view matrix models > #3,0.6403,0.41845,0.64414,149.67,0.76446,-0.42901,-0.4812,129.33,0.074983,0.80053,-0.59459,157.65 > delete: 1-150 Unknown command: delete: 1-150 > delete:1-150 Unknown command: delete:1-150 > delete :1-152 > view matrix models > #3,0.6614,0.42722,0.61646,146.94,0.73189,-0.54731,-0.40594,137.58,0.16397,0.71967,-0.67467,150.65 > select /B 1815 atoms, 1831 bonds, 3 pseudobonds, 236 residues, 2 models selected > cartoon hide (#!3 & sel) > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #2 level 0.09183 > view matrix models > #3,-0.22439,0.94254,-0.24751,163.64,0.41545,0.32228,0.85061,205.39,0.88151,0.08804,-0.46389,117.8 > hide #!3 models > show #!3 models > view matrix models > #3,-0.38686,0.35962,-0.84912,159.16,0.10128,0.93182,0.3485,193.02,0.91656,0.048819,-0.39691,119.12 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.38686,0.35962,-0.84912,168.32,0.10128,0.93182,0.3485,179.29,0.91656,0.048819,-0.39691,120.13 > view matrix models > #3,-0.38686,0.35962,-0.84912,167.76,0.10128,0.93182,0.3485,178.17,0.91656,0.048819,-0.39691,120.25 > view matrix models > #3,-0.38686,0.35962,-0.84912,149.95,0.10128,0.93182,0.3485,182.15,0.91656,0.048819,-0.39691,122.68 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.58964,0.7988,0.11938,203.76,0.69758,0.57817,-0.42319,105.36,-0.40707,-0.16625,-0.89814,206.27 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.58964,0.7988,0.11938,157.09,0.69758,0.57817,-0.42319,93.513,-0.40707,-0.16625,-0.89814,205.42 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.66559,0.74068,0.091572,162.87,0.68199,0.65345,-0.32845,97.779,-0.30312,-0.15616,-0.94007,195.05 > view matrix models > #3,-0.55635,0.78666,0.26767,161.93,0.73855,0.61575,-0.27457,96.749,-0.38081,0.04493,-0.92356,197.78 > view matrix models > #3,-0.34108,0.93634,0.083246,133.06,0.9087,0.35109,-0.22585,91.265,-0.2407,-0.0013876,-0.9706,185.49 > view matrix models > #3,-0.5476,0.68037,-0.48706,126.8,0.78347,0.21255,-0.58395,86.53,-0.29378,-0.70137,-0.64944,219.66 > view matrix models > #3,-0.61182,0.71136,-0.34591,138.04,0.65299,0.20742,-0.72841,89.826,-0.44641,-0.67153,-0.59141,233.79 > view matrix models > #3,-0.59949,0.79471,0.095162,156.76,0.24534,0.29563,-0.92326,110.42,-0.76185,-0.53014,-0.3722,266.18 > view matrix models > #3,-0.25078,0.91118,-0.32689,106.61,0.21957,-0.27534,-0.93594,123.59,-0.94281,-0.30649,-0.13102,287.43 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.25078,0.91118,-0.32689,119.06,0.21957,-0.27534,-0.93594,144.34,-0.94281,-0.30649,-0.13102,277.74 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.01906,0.7899,-0.61293,89.556,0.24367,-0.59089,-0.76907,157.05,-0.96967,-0.16401,-0.18121,274.47 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.01906,0.7899,-0.61293,123.14,0.24367,-0.59089,-0.76907,143.31,-0.96967,-0.16401,-0.18121,277.88 > view matrix models > #3,-0.01906,0.7899,-0.61293,121.13,0.24367,-0.59089,-0.76907,147.34,-0.96967,-0.16401,-0.18121,286.62 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.12704,0.86351,-0.48806,114.25,0.36208,-0.49847,-0.78768,135.28,-0.92345,-0.076653,-0.37598,271.75 > ui tool show ""Fit in Map"" > fitmap sel inMap #1 moveWholeMolecules false Fit molecule 2r6d.pdb (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA- DNA-Hybrid (1).mrc (#1) using 1815 atoms average map value = 0.08333, steps = 160 shifted from previous position = 1.75 rotated from previous position = 13.9 degrees atoms outside contour = 1588, contour level = 0.26541 > fitmap sel inMap #1 Fit molecule 2r6d.pdb (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA- DNA-Hybrid (1).mrc (#1) using 1815 atoms average map value = 0.08331, steps = 80 shifted from previous position = 0.00358 rotated from previous position = 0.00589 degrees atoms outside contour = 1588, contour level = 0.26541 Position of 2r6d.pdb (#3) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc (#1) coordinates: Matrix rotation and translation 0.12703210 0.86354283 -0.48801296 114.24496459 0.36216061 -0.49841152 -0.78767104 135.26517643 -0.92341895 -0.07667956 -0.37605546 271.75285952 Axis 0.73082038 0.44754906 -0.51536531 Axis point 0.00000000 -15.98028024 199.86732761 Rotation angle (degrees) 150.89354619 Shift along axis 3.97835495 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/fitgui.py"", line 651, in _undo position_history.undo() File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 41, in undo if restore_position(ps): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 93, in restore_position atoms.coords = xyz File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 2138 does not match objects array length 0 ValueError: Values array length 2138 does not match objects array length 0 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' See log for complete Python traceback. OpenGL version: 4.1 INTEL-20.2.48 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,4 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0) OS Loader Version: 564.40.4~55 Software: System Software Overview: System Version: macOS 13.1 (22C65) Kernel Version: Darwin 22.2.0 Time since boot: 93 days, 1 hour, 21 minutes Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL S2721Q: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: BM0F513 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 0.00 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Volume Data fixed all ChimeraX