id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15854 Crash on Mac waking from sleep nferraro@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001e8f88c00 (most recent call first): File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension 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All rights reserved. How to cite UCSF ChimeraX > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J905_AMP-PnP-ATP_F-chain.pdb format pdb Chain information for J905_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > open /Users/nicholasferraro/Replicase/Rep_F-chain.pdb format pdb No such file/path: /Users/nicholasferraro/Replicase/Rep_F-chain.pdb > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/Rep_F-chain.pdb Rep_F-chain.pdb title: Cryo-em structure of PCV2 replicase bound to ssDNA [more info...] Chain information for Rep_F-chain.pdb #2 --- Chain | Description | UniProt F | atp-dependent helicase rep | Q6TC59_PCV2 1-314 > hide #2 models > select protein 17548 atoms, 17813 bonds, 1109 residues, 2 models selected > show sel & #!1 cartoons > hide sel & #!1 atoms > select clear > show #2 models > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > select clear Drag select of 1 residues > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.97823,0.20421,0.037036,-21.434,-0.11479,0.68105,-0.72319,125.49,-0.1729,0.70319,0.68966,-13.254 > view matrix models > #2,0.9942,0.081095,0.070677,-14.717,-0.010294,0.72573,-0.6879,100.67,-0.10708,0.68318,0.72236,-24.991 > view matrix models > #2,0.97981,-0.090329,0.17839,-5.8148,0.15712,-0.204,-0.96628,198.71,0.12367,0.97479,-0.18569,1.6759 > view matrix models > #2,0.9939,-0.051726,0.097408,-3.7085,0.10322,0.12502,-0.98677,175.41,0.038864,0.99081,0.1296,-18.943 > view matrix models > #2,0.99261,0.10768,-0.056012,-4.1831,-0.098629,0.44661,-0.88927,164.2,-0.070739,0.88822,0.45393,-24.32 > view matrix models > #2,0.9732,0.21246,-0.087956,-8.6371,-0.22994,0.90125,-0.36725,84.42,0.0012461,0.37763,0.92596,-31.564 > view matrix models > #2,0.95821,0.27598,-0.075235,-14.125,0.2328,-0.59953,0.76575,49.453,0.16623,-0.75127,-0.63872,219.68 > view matrix models > #2,0.89615,0.1669,0.41117,-43.033,0.25916,0.55531,-0.79023,86.051,-0.36022,0.81472,0.45439,29.13 > view matrix models > #2,0.84581,0.20749,0.49149,-47.497,0.30579,0.56636,-0.76533,74.955,-0.43715,0.79761,0.41558,47.088 > view matrix models > #2,0.84319,0.17978,0.50667,-45.783,0.35333,0.52501,-0.77429,72.605,-0.40521,0.83189,0.37916,42.228 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.84319,0.17978,0.50667,-52.163,0.35333,0.52501,-0.77429,66.244,-0.40521,0.83189,0.37916,52.44 > view matrix models > #2,0.84319,0.17978,0.50667,-55.088,0.35333,0.52501,-0.77429,73.009,-0.40521,0.83189,0.37916,64.294 > view matrix models > #2,0.84319,0.17978,0.50667,-55.039,0.35333,0.52501,-0.77429,75.322,-0.40521,0.83189,0.37916,59.161 > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.84972,0.17855,0.49607,-54.859,0.35354,0.50505,-0.78736,78.692,-0.39112,0.84442,0.36603,56.985 > view matrix models > #2,0.66796,0.62915,0.39749,-62.408,0.19932,0.36337,-0.91008,130.39,-0.71701,0.68712,0.11731,150.48 > view matrix models > #2,0.66022,0.63257,0.40492,-62.298,0.23425,0.33881,-0.91123,127.51,-0.71361,0.69646,0.075512,153.27 > view matrix models > #2,0.76323,0.54577,0.34587,-63.602,0.22216,0.28101,-0.93364,137.7,-0.60674,0.78941,0.093226,124.91 > ui mousemode right ""move picked models"" > view matrix models > #2,0.76323,0.54577,0.34587,-60.262,0.22216,0.28101,-0.93364,139.38,-0.60674,0.78941,0.093226,122.78 > view matrix models > #2,0.76323,0.54577,0.34587,-60.982,0.22216,0.28101,-0.93364,138.47,-0.60674,0.78941,0.093226,123.88 > open /Users/nicholasferraro/Replicase/AMP-PnP- > ATP/J905/cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc format > mrc Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc as #3, grid size 300,300,300, pixel 0.844, shown at level 0.107, step 2, values float32 > surface dust #3 size 8.44 > transparency 50 > view matrix models > #2,0.76323,0.54577,0.34587,-48.845,0.22216,0.28101,-0.93364,142.67,-0.60674,0.78941,0.093226,134.31 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.75544,0.56456,0.33252,-48.179,0.20803,0.27458,-0.93879,146.11,-0.62131,0.77838,0.089981,138.09 > view matrix models > #2,0.46987,0.80087,0.37125,-31.262,0.78067,-0.18069,-0.59825,67.268,-0.41204,0.57092,-0.71012,208.58 > ui mousemode right ""move picked models"" > view matrix models #3,1,0,0,0.10035,0,1,0,0.274,0,0,1,-0.95049 > view matrix models > #2,0.46987,0.80087,0.37125,-29.616,0.78067,-0.18069,-0.59825,67.792,-0.41204,0.57092,-0.71012,200.32 > view matrix models > #2,0.46987,0.80087,0.37125,-35.519,0.78067,-0.18069,-0.59825,65.281,-0.41204,0.57092,-0.71012,198.46 > view matrix models #3,1,0,0,-0.17391,0,1,0,0.12879,0,0,1,-0.85748 > view matrix models > #2,0.46987,0.80087,0.37125,-34.756,0.78067,-0.18069,-0.59825,65.58,-0.41204,0.57092,-0.71012,198.99 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.35332,0.90227,0.24713,-13.976,0.74448,-0.11122,-0.65831,70.325,-0.56649,0.41657,-0.71102,239.51 > view matrix models > #2,0.69394,0.70751,0.1337,-36.231,0.26375,-0.076982,-0.96152,174.21,-0.66999,0.70249,-0.24002,177.99 > ui mousemode right ""move picked models"" > view matrix models > #2,0.69394,0.70751,0.1337,-32.11,0.26375,-0.076982,-0.96152,175.48,-0.66999,0.70249,-0.24002,183.52 > ui tool show ""Fit in Map"" > hide #!1 models Opened Rep_F-chain.pdb map 5 as #4, grid size 50,39,43, pixel 1.67, shown at level 0.0982, step 1, values float32 > fitmap #2 inMap #3 resolution 5 Fit map Rep_F-chain.pdb map 5 in map cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc using 4834 points correlation = 0.6136, correlation about mean = 0.09847, overlap = 259.3 steps = 128, shift = 14.9, angle = 10.8 degrees Position of Rep_F-chain.pdb map 5 (#4) relative to cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates: Matrix rotation and translation 0.64300027 0.70128731 0.30780961 -48.78083241 0.41710681 0.01641218 -0.90870927 137.23661534 -0.64231811 0.71268979 -0.28195868 195.46827478 Axis 0.85308013 0.49989857 -0.14951824 Axis point 0.00000000 0.02321171 152.22842263 Rotation angle (degrees) 108.13597115 Shift along axis -2.23564317 Average map value = 0.1444 for 2301 atoms, 1024 outside contour > view matrix models #3,1,0,0,-6.2892,0,1,0,-4.0999,0,0,1,8.6324 > show #!1 models Opened J905_AMP-PnP-ATP_F-chain.pdb map 5 as #5, grid size 68,72,79, pixel 1.67, shown at level 0.107, step 1, values float32 > fitmap #1 inMap #3 resolution 5 Fit map J905_AMP-PnP-ATP_F-chain.pdb map 5 in map cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc using 32348 points correlation = 0.7747, correlation about mean = 0.6944, overlap = 3924 steps = 116, shift = 11.4, angle = 0.135 degrees Position of J905_AMP-PnP-ATP_F-chain.pdb map 5 (#5) relative to cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates: Matrix rotation and translation 0.99999727 -0.00152767 0.00176773 0.04566317 0.00152726 0.99999881 0.00023406 -0.15390765 -0.00176809 -0.00023136 0.99999841 0.27377555 Axis -0.09911389 0.75296278 0.65055629 Axis point 133.64046404 0.00000000 -28.85992112 Rotation angle (degrees) 0.13452723 Shift along axis 0.05769382 Average map value = 0.3812 for 15646 atoms, 2501 outside contour > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.65834,0.67803,0.32691,-50.95,0.38528,0.069564,-0.92018,138.11,-0.64664,0.73174,-0.21543,186.49 > view matrix models > #2,0.88419,0.43034,0.18172,-46.274,0.26527,-0.14235,-0.95361,182.45,-0.38451,0.89137,-0.24002,130.97 > ui mousemode right ""move picked models"" > view matrix models #3,1,0,0,-6.5278,0,1,0,-4.0479,0,0,1,8.4528 > view matrix models #3,1,0,0,-6.152,0,1,0,-4.0428,0,0,1,8.6224 > view matrix models #3,1,0,0,-5.0878,0,1,0,-4.2701,0,0,1,9.4175 > view matrix models #3,1,0,0,-4.8834,0,1,0,-4.1728,0,0,1,9.3867 > view matrix models #3,1,0,0,-4.5536,0,1,0,-4.4886,0,0,1,9.9525 > view matrix models > #2,0.88419,0.43034,0.18172,-54.194,0.26527,-0.14235,-0.95361,175.15,-0.38451,0.89137,-0.24002,129.43 > view matrix models > #2,0.88419,0.43034,0.18172,-54.404,0.26527,-0.14235,-0.95361,174.94,-0.38451,0.89137,-0.24002,129.82 > view matrix models #3,1,0,0,-4.3608,0,1,0,-4.4807,0,0,1,9.7115 > view matrix models > #2,0.88419,0.43034,0.18172,-54.102,0.26527,-0.14235,-0.95361,175.1,-0.38451,0.89137,-0.24002,127.31 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.87678,0.4387,0.197,-55.36,0.29597,-0.16938,-0.94006,171.63,-0.37903,0.88253,-0.27835,131.29 > view matrix models > #2,0.93973,0.27287,0.20601,-49.155,0.27132,-0.22851,-0.93497,181.12,-0.20805,0.93452,-0.28878,99.882 > fitmap #2 inMap #3 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) using 2301 atoms average map value = 0.1186, steps = 112 shifted from previous position = 2.65 rotated from previous position = 7.93 degrees atoms outside contour = 1145, contour level = 0.10709 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates: Matrix rotation and translation 0.96244220 0.26220683 0.07037457 -32.48738924 0.14420491 -0.27411606 -0.95082350 214.52295222 -0.23002162 0.92526102 -0.30163238 94.62985232 Axis 0.98552346 0.15780072 -0.06198743 Axis point 0.00000000 74.98227012 125.80983045 Rotation angle (degrees) 107.85764699 Shift along axis -4.03106931 > select clear > select protein 17548 atoms, 17813 bonds, 1109 residues, 2 models selected Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 1 maps. > select clear > hide #!3 models > select clear > select #2/F:199 24 atoms, 23 bonds, 1 residue, 1 model selected > select #2/F:219 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/F:199 24 atoms, 23 bonds, 1 residue, 1 model selected > select #2/F:195 24 atoms, 25 bonds, 1 residue, 1 model selected > select #2/F:227 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/F:228 24 atoms, 23 bonds, 1 residue, 1 model selected > select #2/F:212 16 atoms, 15 bonds, 1 residue, 1 model selected > select #2/F:251 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/F:193 14 atoms, 13 bonds, 1 residue, 1 model selected > select #2/F:194 21 atoms, 21 bonds, 1 residue, 1 model selected > select #2/F:234 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/F:157 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #2/F:158 18 atoms, 16 bonds, 2 residues, 2 models selected > ui tool show ""Build Structure"" > build join peptide sel length 1.33 omega 180 phi -120 move small > show #!3 models > fitmap #1/F:158-301 inMap #3 Fit molecule J905_AMP-PnP-ATP_F-chain.pdb (#1) to map cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) using 2301 atoms average map value = 0.1473, steps = 140 shifted from previous position = 12 rotated from previous position = 23.4 degrees atoms outside contour = 1030, contour level = 0.10709 Position of J905_AMP-PnP-ATP_F-chain.pdb (#1) relative to cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates: Matrix rotation and translation 0.98548521 -0.02528075 -0.16786838 20.79408241 0.08446934 0.93077082 0.35571141 -43.22013628 0.14725434 -0.36472807 0.91939632 29.58457982 Axis -0.90739448 -0.39689749 0.13823037 Axis point 0.00000000 51.72310976 128.91980738 Rotation angle (degrees) 23.38967573 Shift along axis 2.37501573 > fitmap #1 inMap #3 Fit molecule J905_AMP-PnP-ATP_F-chain.pdb (#1) to map cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) using 17947 atoms average map value = 0.1275, steps = 72 shifted from previous position = 2.8 rotated from previous position = 5.02 degrees atoms outside contour = 10544, contour level = 0.10709 Position of J905_AMP-PnP-ATP_F-chain.pdb (#1) relative to cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates: Matrix rotation and translation 0.97649167 -0.00108788 -0.21555238 25.29628792 0.06579771 0.95376518 0.29326207 -33.02083947 0.20526732 -0.30055082 0.93141534 12.60962435 Axis -0.81246969 -0.57577608 0.09151454 Axis point 0.00000000 15.64232947 115.82216674 Rotation angle (degrees) 21.43447575 Shift along axis -0.38589391 > undo > select #1/F:158-301 2301 atoms, 2341 bonds, 144 residues, 1 model selected > select clear > select #1/F:158-301 2301 atoms, 2341 bonds, 144 residues, 1 model selected > delete atoms sel > close > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix_2/Round_000_real_space_refined_m6_J905_F-chain_001.pdb Chain information for Round_000_real_space_refined_m6_J905_F-chain_001.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > open /Users/nicholasferraro/Replicase/AMP-PnP- > ATP/J905/cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc format > mrc Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc as #2, grid size 300,300,300, pixel 0.844, shown at level 0.107, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > surface dust #2 size 8.44 > style ball Changed 17950 atom styles > show cartoons > hide atoms > ui tool show ""Map Filter"" > volume gaussian #2 sDev 0.76 Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian as #3, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > volume gaussian #2 sDev 1.39 modelId #3 Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian as #3, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > transparency #3.1 50 > close > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J905_AMP-PnP-ATP_F-chain.pdb Chain information for J905_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > show cartoons > hide atoms > show atoms > hide atoms > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/Rep_F-chain.pdb Rep_F-chain.pdb title: Cryo-em structure of PCV2 replicase bound to ssDNA [more info...] Chain information for Rep_F-chain.pdb #2 --- Chain | Description | UniProt F | atp-dependent helicase rep | Q6TC59_PCV2 1-314 > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > open /Users/nicholasferraro/Replicase/AMP-PnP- > ATP/J905/cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc format > mrc Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc as #3, grid size 300,300,300, pixel 0.844, shown at level 0.107, step 2, values float32 > surface dust #3 size 8.44 > select clear > hide #2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #1 inMap #3 Fit molecule J905_AMP-PnP-ATP_F-chain.pdb (#1) to map cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) using 15646 atoms average map value = 0.3812, steps = 48 shifted from previous position = 0.124 rotated from previous position = 0.177 degrees atoms outside contour = 2503, contour level = 0.10709 Position of J905_AMP-PnP-ATP_F-chain.pdb (#1) relative to cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc (#3) coordinates: Matrix rotation and translation 0.99999542 -0.00243404 0.00179942 0.17598289 0.00243298 0.99999686 0.00059298 -0.29408400 -0.00180085 -0.00058860 0.99999821 0.33565761 Axis -0.19156142 0.58368756 0.78905833 Axis point 135.24453505 76.72786250 0.00000000 Rotation angle (degrees) 0.17670461 Shift along axis 0.05948873 > transparency 50 > volume gaussian #3 sDev 1.39 Opened cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian as #4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > transparency #4.1 50 > show #2 models > select add #2 2301 atoms, 2341 bonds, 144 residues, 1 model selected > ui mousemode right ""move picked models"" Drag select of 5 residues > select add #2 2301 atoms, 2341 bonds, 144 residues, 1 model selected > view matrix models #2,1,0,0,1.5068,0,1,0,2.2802,0,0,1,15.38 > view matrix models #2,1,0,0,1.2791,0,1,0,3.2749,0,0,1,25.757 > view matrix models #2,1,0,0,-0.18983,0,1,0,14.812,0,0,1,23.838 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.99873,-0.017665,-0.047249,6.6937,0.016424,0.99951,-0.026542,14.987,0.047695,0.025733,0.99853,13.769 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.99873,-0.017665,-0.047249,2.7487,0.016424,0.99951,-0.026542,12.487,0.047695,0.025733,0.99853,12.857 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.99939,-0.027994,-0.02093,1.0038,0.027057,0.99867,-0.043806,12.663,0.022129,0.043213,0.99882,15.077 > view matrix models > #2,0.98232,-0.1785,-0.056455,22.9,0.17837,0.98394,-0.0074561,-13.551,0.056879,-0.0027456,0.99838,14.356 > fitmap #2 inMap #4 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian (#4) using 2301 atoms average map value = 0.1539, steps = 64 shifted from previous position = 0.797 rotated from previous position = 6.05 degrees atoms outside contour = 675, contour level = 0.11785 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J905_004_volume_map_sharp_fit.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.99133997 -0.13046432 0.01497075 9.92324272 0.12948941 0.99011553 0.05388618 -12.88758147 -0.02185299 -0.05148097 0.99843485 31.99752721 Axis -0.37244959 0.13016380 0.91887904 Axis point 134.04284684 135.75984104 -0.00000000 Rotation angle (degrees) 8.13185002 Shift along axis 24.02845280 > select clear > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > view matrix models > #2,0.9911,-0.1315,0.020838,9.4648,0.13043,0.99038,0.046314,-12.284,-0.026728,-0.043183,0.99871,31.886 > ui mousemode right ""move picked models"" > view matrix models > #2,0.9911,-0.1315,0.020838,8.4969,0.13043,0.99038,0.046314,-13.015,-0.026728,-0.043183,0.99871,32.385 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.99122,-0.1299,-0.024746,13,0.13023,0.99141,0.012021,-9.5644,0.022972,-0.015137,0.99962,21.514 > select clear > hide #!4 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1 > close #1 > close #3 > close #4 > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-PnP- ATP/AMP-PnP-ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb --- warnings | Cannot find LINK/SSBOND residue LYS (180 ) Cannot find LINK/SSBOND residue SER (181 ) Chain information for J906_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > open /Users/nicholasferraro/Replicase/AMP-PnP- > ATP/J906/cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc Opened cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 0.844, shown at level 0.102, step 2, values float32 > surface dust #3 size 8.44 > volume gaussian #3 sDev 1.39 Opened cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian as #4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > style ball Changed 17948 atom styles > show cartoons > hide atoms > volume #!4 style image > volume #!4 style surface > transparency #4.1 50 > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > fitmap #2 inMap #4 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian (#4) using 2301 atoms average map value = 0.1512, steps = 148 shifted from previous position = 13.4 rotated from previous position = 11.3 degrees atoms outside contour = 694, contour level = 0.11036 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.95170411 -0.29988927 0.06577020 18.86607318 0.29806581 0.95385834 0.03620833 -39.77252537 -0.07359394 -0.01485577 0.99717764 28.17895433 Axis -0.08288271 0.22620348 0.97054750 Axis point 152.82341965 42.93857940 0.00000000 Rotation angle (degrees) 17.94177732 Shift along axis 16.78865879 > view matrix models > #2,0.94285,-0.32663,0.065855,23.021,0.331,0.94085,-0.072441,-32.481,-0.038298,0.090099,0.9952,11.951 > fitmap #2 inMap #4 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian (#4) using 2301 atoms average map value = 0.1512, steps = 80 shifted from previous position = 0.255 rotated from previous position = 6.54 degrees atoms outside contour = 694, contour level = 0.11036 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J906_004_volume_map_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.95166220 -0.30016098 0.06513401 18.95505007 0.29835014 0.95377072 0.03617461 -39.79295834 -0.07298111 -0.01499327 0.99722062 28.08533074 Axis -0.08301514 0.22407900 0.97102888 Axis point 152.67497169 43.20409743 0.00000000 Rotation angle (degrees) 17.94982358 Shift along axis 16.78134491 > hide #!4 models > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1 > close #1 > hide #2 models > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-PnP- ATP/AMP-PnP-ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 121 LEU A 127 1 7 Start residue of secondary structure not found: HELIX 2 2 LEU A 132 GLN A 138 1 7 Start residue of secondary structure not found: HELIX 3 3 VAL A 141 VAL A 144 1 4 Start residue of secondary structure not found: HELIX 4 4 ARG A 148 SER A 157 1 10 Start residue of secondary structure not found: HELIX 5 5 SER A 181 ASN A 186 1 6 2 messages similar to the above omitted End residue of secondary structure not found: HELIX 39 39 ARG F 148 SER F 157 1 10 Start residue of secondary structure not found: SHEET 1 1 1 ASN A 168 VAL A 173 0 Start residue of secondary structure not found: SHEET 1 2 1 THR A 193 TRP A 195 0 Start residue of secondary structure not found: SHEET 1 3 1 VAL A 212 PHE A 217 0 Start residue of secondary structure not found: SHEET 1 4 1 SER A 250 SER A 255 0 Start residue of secondary structure not found: SHEET 1 5 1 SER A 280 PHE A 283 0 notes | Combining 3 symmetry atoms into MG /C:401 MG Combining 3 symmetry atoms into MG /B:401 MG Combining 3 symmetry atoms into MG /D:401 MG Combining 3 symmetry atoms into MG /A:401 MG Chain information for J906_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description B C E I J K N O P Q T | No description available D L R | No description available F | No description available G | No description available M S | No description available > style #!1 ball Changed 46286 atom styles > select #1/I 2969 atoms, 3015 bonds, 186 residues, 1 model selected > select #1/T 2958 atoms, 3004 bonds, 186 residues, 1 model selected > select #1/E:235@CG 1 atom, 1 residue, 1 model selected > select #1/T 2958 atoms, 3004 bonds, 186 residues, 1 model selected > view matrix models > #1,1,0.00051083,0.00089905,-0.1864,-0.00050689,0.99999,-0.0043795,0.6425,-0.00090128,0.004379,0.99999,-0.46758 > view matrix models > #1,1,0.00051083,0.00089905,-0.15951,-0.00050689,0.99999,-0.0043795,0.65177,-0.00090128,0.004379,0.99999,-0.50336 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/S 589 atoms, 592 bonds, 38 residues, 1 model selected > select #1/D:156@CG2 1 atom, 1 residue, 1 model selected > select #1/S 589 atoms, 592 bonds, 38 residues, 1 model selected > view matrix models > #1,1,0.00052342,0.0014962,-0.2394,-0.00051361,0.99998,-0.0065486,0.93866,-0.0014996,0.0065478,0.99998,-0.71387 > select add #1/F:128@HB3 590 atoms, 592 bonds, 39 residues, 1 model selected > view matrix models > #1,1,-0.0015512,0.0013835,0.054038,0.0015635,0.99996,-0.0089234,0.9783,-0.0013696,0.0089255,0.99996,-1.0479 > view matrix models > #1,1,-0.00057657,-0.00023451,0.13508,0.00057417,0.99995,-0.010146,1.2707,0.00024035,0.010146,0.99995,-1.423 > view matrix models > #1,0.9999,0.0065703,-0.012238,0.76213,-0.0068038,0.99979,-0.019138,3.4451,0.01211,0.01922,0.99974,-4.182 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/S 589 atoms, 592 bonds, 38 residues, 1 model selected > select #1/F:120@C 1 atom, 1 residue, 1 model selected > select #1/S 589 atoms, 592 bonds, 38 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add #1/F:120@C 590 atoms, 592 bonds, 39 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/R 2983 atoms, 3031 bonds, 187 residues, 1 model selected > select add #1/D:121@OG1 2984 atoms, 3031 bonds, 188 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/Q 2969 atoms, 3015 bonds, 186 residues, 1 model selected > select add #1/C:121@OG1 2970 atoms, 3015 bonds, 187 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/P 2970 atoms, 3016 bonds, 186 residues, 1 model selected > select add #1/B:140@CG 2971 atoms, 3016 bonds, 187 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/O 2969 atoms, 3015 bonds, 186 residues, 1 model selected > select add #1/I:119@CG 2970 atoms, 3015 bonds, 187 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/N 2958 atoms, 3004 bonds, 186 residues, 1 model selected > select add #1/E:120@OG 2959 atoms, 3004 bonds, 187 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/M 589 atoms, 592 bonds, 38 residues, 1 model selected > select add #1/F:119@HG 590 atoms, 592 bonds, 39 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/L 2983 atoms, 3031 bonds, 187 residues, 1 model selected > select add #1/D:121@CG2 2984 atoms, 3031 bonds, 188 residues, 1 model selected > select subtract #1/D:121@CG2 2983 atoms, 3031 bonds, 187 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add #1/D:121@CG2 2984 atoms, 3031 bonds, 188 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/I 2967 atoms, 3011 bonds, 186 residues, 1 model selected > select #1/K 2969 atoms, 3015 bonds, 186 residues, 1 model selected > select add #1/C:289@OE2 2970 atoms, 3015 bonds, 187 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/J 2970 atoms, 3016 bonds, 186 residues, 1 model selected > select add #1/B:145@CZ 2971 atoms, 3016 bonds, 187 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete bonds sel The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete bonds sel The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb models #1 relModel #1 > select #1/G 582 atoms, 615 bonds, 2 pseudobonds, 18 residues, 2 models selected > select #1/I 2967 atoms, 3011 bonds, 186 residues, 1 model selected > select subtract #1/I:119@CD2 2966 atoms, 3008 bonds, 186 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/I:119@CD2 1 atom, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add #1/A:303@CB 1 atom, 1 bond, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add #1/A:303@HB3 2 atoms, 1 bond, 1 residue, 1 model selected > select add #1/A:303@N 3 atoms, 1 bond, 1 residue, 1 model selected > select add #1/A:303@C 4 atoms, 1 bond, 1 residue, 1 model selected > select add #1/A:303@O 5 atoms, 1 bond, 1 residue, 1 model selected > select add #1/A:303@CA 6 atoms, 1 bond, 1 residue, 1 model selected > select add #1/A:303@HA 7 atoms, 2 bonds, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb models #1 relModel #1 > close #1 > close #3-4 > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J906_AMP-PnP-ATP_F-chain.pdb Chain information for J906_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > style #!1 ball Changed 18314 atom styles > select protein 19827 atoms, 20128 bonds, 1 pseudobond, 1253 residues, 3 models selected > show sel & #!1 cartoons > hide sel & #!1 atoms > select clear > select #1/F:180 22 atoms, 21 bonds, 1 residue, 1 model selected > select #1/F:179 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > view matrix models > #1,1,1.1084e-05,-0.00078809,0.10147,-9.4237e-06,1,0.0021073,-0.27362,0.00078811,-0.0021073,1,0.178 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete bonds sel The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete bonds sel > select ligand 202 atoms, 212 bonds, 5 residues, 1 model selected > select nucleic-acid 582 atoms, 615 bonds, 2 pseudobonds, 18 residues, 2 models selected > color sel byhetero > color (#!1 & sel) dim gray > color sel byhetero > select clear > close #1 > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J907_AMP-PnP-ATP_F-chain.pdb Chain information for J907_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > select protein 17548 atoms, 17813 bonds, 1109 residues, 2 models selected > style sel & #!1 ball Changed 15247 atom styles > show sel & #!1 cartoons > hide sel & #!1 atoms > select clear > show #2 models > open /Users/nicholasferraro/Replicase/AMP-PnP- > ATP/J907/cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc Opened cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 0.844, shown at level 0.128, step 2, values float32 > surface dust #3 size 8.44 > volume gaussian #3 sDev 1.39 Opened cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc gaussian as #4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > transparency #4.1 50 > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > ui mousemode right ""translate selected models"" > ui mousemode right ""move picked models"" Drag select of 4 residues, 4 cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc gaussian > select clear > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > view matrix models > #2,0.95166,-0.30016,0.065134,23.953,0.29835,0.95377,0.036175,-37.253,-0.072981,-0.014993,0.99722,27.614 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.94317,-0.3102,0.11918,20.779,0.30644,0.95062,0.049143,-39.544,-0.12854,-0.0098279,0.99166,36.465 > fitmap #2 inMap #4 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc gaussian (#4) using 2301 atoms average map value = 0.2168, steps = 64 shifted from previous position = 4.29 rotated from previous position = 4.89 degrees atoms outside contour = 620, contour level = 0.13548 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J907_006_volume_map_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.93427765 -0.35235322 0.05452054 29.32605372 0.34699294 0.93371156 0.08819650 -48.95454813 -0.08198278 -0.06348177 0.99460992 36.00893891 Axis -0.20820387 0.18737370 0.95996992 Axis point 163.74077607 64.08526484 0.00000000 Rotation angle (degrees) 21.36169254 Shift along axis 19.28890544 > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1 > close #4 > close #3 > close #1 > hide #2 models > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J907_AMP-PnP-ATP_F-chain.pdb Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP-PnP- ATP/AMP-PnP-ATP_Models_Phenix/J907_AMP-PnP-ATP_F-chain.pdb --- warnings | Start residue of secondary structure not found: HELIX 36 36 THR F 121 LEU F 127 1 7 Start residue of secondary structure not found: HELIX 37 37 LEU F 132 GLN F 138 1 7 Start residue of secondary structure not found: HELIX 38 38 VAL F 141 VAL F 144 1 4 Start residue of secondary structure not found: HELIX 39 39 ARG F 148 SER F 157 1 10 Chain information for J907_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description A B C E | No description available D | No description available G | No description available f | No description available > select protein 19844 atoms, 20150 bonds, 1253 residues, 2 models selected > style sel & #!1 ball Changed 17543 atom styles > show sel & #!1 cartoons > hide sel & #!1 atoms > select clear > show #2 models > hide #2 models > close #1 > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J908_AMP-PnP-ATP_F-chain.pdb Chain information for J908_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > select protein 17541 atoms, 17806 bonds, 1109 residues, 2 models selected > style sel & #!1 ball Changed 15240 atom styles > hide sel & #!1 atoms > show sel & #!1 cartoons > show #2 models > select clear > open /Users/nicholasferraro/Replicase/AMP-PnP- > ATP/J908/cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 0.844, shown at level 0.109, step 2, values float32 > surface dust #3 size 8.44 > volume gaussian #3 sDev 1.39 Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian as #4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > volume gaussian #3 sDev 1.99 modelId #4 Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian as #4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > transparency #4.1 50 > volume #4 level 0.1774 > select add #2 2301 atoms, 2341 bonds, 144 residues, 1 model selected > fitmap #2 inMap #4 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) using 2301 atoms average map value = 0.1902, steps = 68 shifted from previous position = 1.83 rotated from previous position = 1.73 degrees atoms outside contour = 975, contour level = 0.17737 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.94045145 -0.33383660 0.06406395 24.53146002 0.32978649 0.94173541 0.06614591 -45.91724457 -0.08241322 -0.04107959 0.99575124 32.61711383 Axis -0.15585028 0.21290186 0.96456389 Axis point 160.17273027 53.25130062 0.00000000 Rotation angle (degrees) 20.12086339 Shift along axis 17.86218855 > volume #4 level 0.1225 > ui mousemode right ""move picked models"" > view matrix models #4,1,0,0,0.25077,0,1,0,0.11398,0,0,1,0.13124 > view matrix models > #2,0.94045,-0.33384,0.064064,26.5,0.32979,0.94174,0.066146,-44.84,-0.082413,-0.04108,0.99575,30.444 > view matrix models > #2,0.94045,-0.33384,0.064064,25.836,0.32979,0.94174,0.066146,-44.589,-0.082413,-0.04108,0.99575,31.493 > fitmap #2 inMap #4 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) using 2301 atoms average map value = 0.1902, steps = 88 shifted from previous position = 2.04 rotated from previous position = 0.00579 degrees atoms outside contour = 452, contour level = 0.12253 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.94044719 -0.33386547 0.06397604 24.54360099 0.32981553 0.94172227 0.06618827 -45.92387749 -0.08234564 -0.04114628 0.99575408 32.61095523 Axis -0.15599976 0.21266355 0.96459229 Axis point 160.17382780 53.28833140 0.00000000 Rotation angle (degrees) 20.12207655 Shift along axis 17.86114518 > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J908_AMP-PnP-ATP_F-chain.pdb models #2 relModel #1 > close #1 > close #3 > close #4 > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix_2/Round_000_real_space_refined_m5_J908_F-chain_001.pdb Chain information for Round_000_real_space_refined_m5_J908_F-chain_001.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > hide #2 models > select #1/F:158-301 2237 atoms, 2277 bonds, 144 residues, 1 model selected > select subtract #1/F:187@CZ 2236 atoms, 2274 bonds, 144 residues, 1 model selected > select subtract #1/F:275@H 2235 atoms, 2273 bonds, 144 residues, 1 model selected > select subtract #1/F:301@C 2234 atoms, 2271 bonds, 144 residues, 1 model selected > select subtract #1/F:301@H 2233 atoms, 2270 bonds, 144 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #1/F:187@CZ 1 atom, 1 residue, 1 model selected > select subtract #1/F:187@CZ Nothing selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/F:187@CZ 1 atom, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select add #1/F:301@C 1 atom, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select protein 17541 atoms, 17806 bonds, 1109 residues, 2 models selected > style sel & #!1 ball Changed 15240 atom styles > hide sel & #!1 atoms > show sel & #!1 cartoons > select clear > hide #!1 models > show #2 models > show #!1 models > hide #2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J908_AMP-PnP-ATP_F-chain.pdb models #1 relModel #1 > open /Users/nicholasferraro/Replicase/AMP-PnP- > ATP/J908/cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 0.844, shown at level 0.109, step 2, values float32 > surface dust #3 size 8.44 > volume gaussian #3 sDev 1.99 Opened cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian as #4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > volume #4 level 0.08933 > transparency #4.1 50 > volume #4 level 0.1168 > show #2 models > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > fitmap #2 inMap #4 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) using 2301 atoms average map value = 0.1902, steps = 48 shifted from previous position = 0.305 rotated from previous position = 0.0154 degrees atoms outside contour = 404, contour level = 0.11684 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J908_005_volume_map_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.94043423 -0.33395056 0.06372200 24.57937352 0.32990985 0.94168804 0.06620525 -45.93622576 -0.08211552 -0.04123916 0.99576924 32.58286412 Axis -0.15613959 0.21193296 0.96473045 Axis point 160.14850085 53.38733438 0.00000000 Rotation angle (degrees) 20.12474429 Shift along axis 17.86046749 > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/Rep_F-chain.pdb models #2 relModel #1 > close #1 > close #4 > close #3 > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/J909_AMP-PnP-ATP_F-chain.pdb Chain information for J909_AMP-PnP-ATP_F-chain.pdb #1 --- Chain | Description A B C E | No description available D | No description available F | No description available G | No description available > open /Users/nicholasferraro/Replicase/AMP-PnP- > ATP/J909/cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc Opened cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 0.844, shown at level 0.112, step 2, values float32 > surface dust #3 size 8.44 > volume gaussian #3 sDev 1.99 Opened cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc gaussian as #4, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > transparency #4.1 50 > select #2/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > fitmap #2 inMap #4 Fit molecule Rep_F-chain.pdb (#2) to map cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc gaussian (#4) using 2301 atoms average map value = 0.1186, steps = 72 shifted from previous position = 3.6 rotated from previous position = 3.5 degrees atoms outside contour = 1348, contour level = 0.12932 Position of Rep_F-chain.pdb (#2) relative to cryosparc_P5_cryosparc_P5_J909_005_volume_map_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.95235909 -0.30219235 0.04113324 23.49737932 0.29631370 0.94876734 0.10972113 -43.63966789 -0.07218276 -0.09230557 0.99311094 38.86709029 Axis -0.31479762 0.17656878 0.93259097 Axis point 172.42758410 72.59977955 0.00000000 Rotation angle (degrees) 18.71636147 Shift along axis 21.14477536 > view matrix models > #2,0.95236,-0.30219,0.041133,22.889,0.29631,0.94877,0.10972,-47.041,-0.072183,-0.092306,0.99311,46.721 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.94819,-0.31675,0.024549,26.758,0.31147,0.94205,0.12463,-50.284,-0.062602,-0.11052,0.9919,47.207 > view matrix models > #2,0.96067,-0.24914,-0.12267,32.937,0.25357,0.96707,0.021704,-33.102,0.11322,-0.051955,0.99221,13.245 > ui mousemode right ""move picked models"" > view matrix models #4,1,0,0,0.18634,0,1,0,-0.01177,0,0,1,0.3745 > view matrix models > #2,0.96067,-0.24914,-0.12267,32.915,0.25357,0.96707,0.021704,-31.626,0.11322,-0.051955,0.99221,9.3094 > view matrix models > #2,0.96067,-0.24914,-0.12267,35.94,0.25357,0.96707,0.021704,-28.517,0.11322,-0.051955,0.99221,7.8589 > volume #4 level 0.086 > view matrix models > #2,0.96067,-0.24914,-0.12267,36.429,0.25357,0.96707,0.021704,-30.474,0.11322,-0.051955,0.99221,6.4883 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.95181,-0.29273,-0.091415,39.12,0.29757,0.95366,0.044463,-38.408,0.074164,-0.069523,0.99482,14.228 > view matrix models > #2,0.95143,-0.30018,0.068362,23.521,0.30763,0.93563,-0.17307,-15.776,-0.012011,0.18569,0.98253,2.8138 > view matrix models > #2,0.95953,-0.27955,0.033907,23.649,0.2781,0.92178,-0.27014,0.31878,0.044263,0.26864,0.96222,-12.585 > view matrix models > #2,0.95996,-0.27835,0.031671,23.688,0.27605,0.92062,-0.27613,1.3785,0.047704,0.27382,0.9606,-13.498 > view matrix models > #2,0.9647,-0.26333,0.00085811,24.553,0.24646,0.90172,-0.35518,16.151,0.092757,0.34286,0.9348,-25.117 > view matrix models > #2,0.96312,-0.26906,-0.0033581,25.829,0.24991,0.89907,-0.35947,16.317,0.099735,0.34537,0.93315,-26.314 > view matrix models > #2,0.96313,-0.26902,-0.0032043,25.807,0.24991,0.899,-0.35965,16.344,0.099633,0.34559,0.93308,-26.313 > volume #4 level 0.1072 > hide #2 models > select protein 17540 atoms, 17805 bonds, 1109 residues, 2 models selected > style sel & #!1 ball Changed 15239 atom styles > hide sel & #!1 atoms > show sel & #!1 cartoons > show #2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [deleted to fit within ticket limits] > morph #1,7,6,3,10,5,4 frames 7 Computed 43 frame morph #11 > coordset #11 1,43 > hide #!8 models > show #!8 models > hide #!11 models > show #!11 models > hide #!8 models > hide #!11 models > show #!5 models > show #!4 models > show #!10 models > hide #!4 models > hide #!5 models > show #!4 models > hide #!4 models > show #!4 models > hide #!10 models > show #!5 models > hide #!5 models > show #!5 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > morph #1,7,6,3,5,4,10 frames 7 Computed 43 frame morph #12 > coordset #12 1,43 > morph #1,7,6,3,frames 4 Missing or invalid ""structures"" argument: only initial part ""#1,7,6,3"" of atom specifier valid > morph #1,7,6,3 frames 4 Computed 13 frame morph #13 > coordset #13 1,13 > hide #!12 models > hide #!13 models > show #!13 models > show #!12 models > hide #!13 models > show #!13 models > hide #!12 models > hide #!13 models > show #!6 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > show #!5 models > hide #!3 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!3 models > hide #!6 models > morph #1,7,6,5,3 frames 4 Computed 17 frame morph #14 > coordset #14 1,17 > show #!3 models > hide #!14 models > show #!1 models > hide #!1 models > show #!4 models > hide #!4 models > show #!10 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > morph #1,7,6,5,3,4,10 frames 4 Computed 25 frame morph #15 > coordset #15 1,25 > morph #1,7,6,5,3,4,10 frames 7 Computed 43 frame morph #16 > coordset #16 1,43 > morph #1,7,6,5,3,10,4 frames 7 Computed 43 frame morph #17 > coordset #17 1,43 > morph #1,7,6,5,3,4,10frames 7 Missing or invalid ""structures"" argument: only initial part ""#1,7,6,5,3,4"" of atom specifier valid > morph #1,7,6,5,3,4,10 frames 7 Computed 43 frame morph #18 > coordset #18 1,43 > hide #!18 models > hide #!17 models > hide #!16 models > show #!3 models > hide #!15 models > show #!10 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!3 models > show #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > show #!3 models > hide #!10 models > show #!4 models > hide #!4 models > show #!10 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > show #!3 models > hide #!3 models > hide #!10 models > show #!3 models > show #!10 models > show #!4 models > hide #!4 models > hide #!3 models > hide #!10 models > show #!5 models > show #!4 models > hide #!4 models > show #!4 models > morph #1,7,6,5,4,3,10 frames 7 Computed 43 frame morph #19 > coordset #19 1,43 > morph #1,7,6,5,4,10,3 frames 7 Computed 43 frame morph #20 > coordset #20 1,43 > hide #!19 models > show #!19 models > hide #!20 models > hide #!19 models > show #!20 models > select nucleic-acid 4254 atoms, 4454 bonds, 2 pseudobonds, 132 residues, 21 models selected > hide sel & #!20 cartoons > select clear > morph #1,7,6,5,3,4,10frames 7 Missing or invalid ""structures"" argument: only initial part ""#1,7,6,5,3,4"" of atom specifier valid > morph #1,7,6,5,3,4,10 frames 7 Computed 43 frame morph #21 > coordset #21 1,43 > hide #!20 models > morph #7,1,6,5,3,4,10 frames 7 Computed 43 frame morph #22 > coordset #22 1,43 > hide #!21 models > morph #7,6,1,5,3,4,10 frames 7 Computed 43 frame morph #23 > coordset #23 1,43 > hide #!22 models > morph #7,1,6,5,3,4,10 frames 7 Computed 43 frame morph #24 > coordset #24 1,43 > hide #!23 models > select nucleic-acid 5026 atoms, 5258 bonds, 2 pseudobonds, 156 residues, 25 models selected > hide sel & #!24 cartoons > select clear > morph #1,7,6,5,3,4,10 frames 7 Computed 43 frame morph #25 > coordset #25 1,43 > hide #!24 models > close #2,11-25 > close #8-9 > show #!10 models > show #!4 models > hide #!4 models > show #!4 models > hide #!10 models > show #!10 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!10 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > show #!4 models > show #!3 models > hide #!3 models > hide #!4 models > show #!3 models > show #!4 models > show #!5 models > hide #!4 models > hide #!3 models > show #!4 models > show #!3 models > hide #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > show #!10 models > hide #!10 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!4 models > hide #!3 models > show #!4 models > show #!3 models > hide #!3 models > hide #!4 models > show #!4 models > show #!3 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > morph #1,7,6,5,4,3,10 frames 7 Computed 43 frame morph #2 > coordset #2 1,43 > hide #!2 models > show #!3 models > show #!10 models > hide #!10 models > hide #!3 models > show #!10 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 > morph #1,7,6,5,4,10,3 frames 7 Computed 43 frame morph #8 > coordset #8 1,43 > morph #1,7,6,5,4,10 frames 7 Computed 36 frame morph #9 > coordset #9 1,36 > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!8 models > hide #!9 models > show #!1 models > show #!7 models > show #!6 models > show #!5 models > show #!4 models > show #!10 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!10 models > show #!10 models > morph #1,7,6,5,3,4,10 frames 7 Computed 43 frame morph #11 > coordset #11 1,43 > morph #1,7,6,5,3,4,10 frames 7 Computed 43 frame morph #12 > coordset #12 1,43 > morph #1,7,6,5,3,4 frames 7 Computed 36 frame morph #13 > coordset #13 1,36 > hide #!11 models > hide #!12 models > morph #1,7,6,5,4,3,10 frames 7 Computed 43 frame morph #14 > coordset #14 1,43 > hide #!13 models > hide #!14 models > show #!5 models > show #!4 models > show #!3 models > hide #!3 models > hide #!4 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > show #!10 models > morph #1,7,6,5,3,4,10 frames 7 Computed 43 frame morph #15 > coordset #15 1,43 > morph #1,7,6,5,3,4 frames 7 Computed 36 frame morph #16 > coordset #16 1,36 > hide #!15 models > show #!15 models > hide #!16 models > hide #!15 models > show #!5 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > hide #!5 models > show #!5 models > hide #!4 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 > show #!4 models > hide #!4 models > show #!4 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!4 models > hide #!3 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > close #2,8-9,11-16 > hide #!10 models > show #!7 models > hide #!7 models > show #!6 models > hide #!6 models > show #!4 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!4 models > hide #!10 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > show #!10 models > hide #!10 models > hide #!4 models > hide #!3 models > show #!3 models > show #!4 models > show #!10 models > hide #!10 models > hide #!4 models > hide #!3 models > show #!7 models > hide #!7 models > show #!1 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > ui tool show Matchmaker > matchmaker #7/C to #1/C pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker J905_AMP-PnP-ATP_F-chain.pdb, chain C (#1) with J922_AMP-PnP-ATP_F- chain.pdb, chain C (#7), sequence alignment score = 870.8 RMSD between 183 pruned atom pairs is 0.650 angstroms; (across all 185 pairs: 0.694) > show #!7 models > ui tool show Matchmaker > matchmaker #7/C to #1/C pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker J905_AMP-PnP-ATP_F-chain.pdb, chain C (#1) with J922_AMP-PnP-ATP_F- chain.pdb, chain C (#7), sequence alignment score = 870.8 RMSD between 183 pruned atom pairs is 0.650 angstroms; (across all 185 pairs: 0.694) > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!1 models > show #!7 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!7 models > show #!7 models > show #!6 models > show #!5 models > hide #!5 models > show #!5 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > show #!3 models > show #!4 models > show #!10 models > hide #!4 models > hide #!10 models > hide #!3 models > show #!4 models > show #!3 models > show #!10 models > morph #1,7,6,5,4,3,10 frames 7 Computed 43 frame morph #2 > coordset #2 1,43 > show #!1 models > hide #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > hide #!1 models > show #!2 models > select nucleic-acid 1938 atoms, 2042 bonds, 2 pseudobonds, 60 residues, 9 models selected > hide sel & #!2 cartoons > select clear > ui tool show ""Side View"" > ui tool show ""Show Sequence Viewer"" > sequence chain #1/F #4/F #5/F #6/F #7/F #3/F #10/F #2/F Alignment identifier is 1 > hide #!2 models > show #!1 models > show #!7 models > hide #!7 models > show #!7 models > show #!6 models > hide #!7 models > hide #!6 models > show #!2 models > hide #!1 models > hide #!2 models > show #!7 models > hide #!7 models > show #!2 models > morph #7,1,5,4,3 frames 7 Computed 29 frame morph #8 > coordset #8 1,29 > hide #!2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!8 models > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968-RSR-Regclash-out- > coot-2.pdb Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP- PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968-RSR-Regclash-out- coot-2.pdb --- warnings | Duplicate atom serial number found: 9340 Duplicate atom serial number found: 12880 Duplicate atom serial number found: 13463 Chain information for J968-RSR-Regclash-out-coot-2.pdb #9 --- Chain | Description A B C D E | No description available F | No description available G | No description available > select #9/F:119-157 600 atoms, 603 bonds, 39 residues, 1 model selected > select subtract #9/F:128@HB2 599 atoms, 602 bonds, 39 residues, 1 model selected > select subtract #9/F:128@CA 598 atoms, 598 bonds, 39 residues, 1 model selected > select subtract #9/F:128@O 597 atoms, 597 bonds, 39 residues, 1 model selected > select subtract #9/F:154@CA 596 atoms, 593 bonds, 39 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #9/F:154@CA 1 atom, 1 residue, 1 model selected > select subtract #9/F:154@CA Nothing selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #9/F:154@CA 1 atom, 1 residue, 1 model selected > select subtract #9/F:154@CA Nothing selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #9/F:154@CA 1 atom, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #9/F:128@O 1 atom, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > select #9/F:128@CA 1 atom, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete atoms sel > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J968_with_FOD/cryosparc_P5_J968_004_volume_map_sharp_inv.mrc Opened cryosparc_P5_J968_004_volume_map_sharp_inv.mrc as #11, grid size 300,300,300, pixel 0.844, shown at level 0.166, step 2, values float32 > surface dust #11 size 8.44 > fitmap #9 inMap #11 Fit molecule J968-RSR-Regclash-out-coot-2.pdb (#9) to map cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) using 15253 atoms average map value = 0.5132, steps = 44 shifted from previous position = 0.0145 rotated from previous position = 0.0499 degrees atoms outside contour = 2472, contour level = 0.16566 Position of J968-RSR-Regclash-out-coot-2.pdb (#9) relative to cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) coordinates: Matrix rotation and translation 0.99999976 -0.00052808 -0.00044255 0.11393674 0.00052832 0.99999972 0.00053171 -0.13591873 0.00044227 -0.00053194 0.99999976 0.01360411 Axis -0.61102746 -0.50829386 0.60686307 Axis point 0.00000000 16.65081026 248.25080303 Rotation angle (degrees) 0.04986914 Shift along axis 0.00772401 > fitmap #9 inMap #11 Fit molecule J968-RSR-Regclash-out-coot-2.pdb (#9) to map cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) using 15253 atoms average map value = 0.5132, steps = 40 shifted from previous position = 0.0164 rotated from previous position = 0.0151 degrees atoms outside contour = 2457, contour level = 0.16566 Position of J968-RSR-Regclash-out-coot-2.pdb (#9) relative to cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) coordinates: Matrix rotation and translation 0.99999980 -0.00035946 -0.00051458 0.11169757 0.00035983 0.99999967 0.00072154 -0.15049025 0.00051432 -0.00072173 0.99999961 0.02863936 Axis -0.75450829 -0.53788310 0.37603060 Axis point 0.00000000 35.69548994 203.03796385 Rotation angle (degrees) 0.05479953 Shift along axis 0.00743869 > ui tool show ""Fit in Map"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Opened J968-RSR-Regclash-out-coot-2.pdb map 5 as #12, grid size 65,67,76, pixel 1.67, shown at level 0.114, step 1, values float32 > fitmap #9 inMap #11 resolution 5 Fit map J968-RSR-Regclash-out-coot-2.pdb map 5 in map cryosparc_P5_J968_004_volume_map_sharp_inv.mrc using 30785 points correlation = 0.8206, correlation about mean = 0.6727, overlap = 5513 steps = 40, shift = 0.068, angle = 0.0282 degrees Position of J968-RSR-Regclash-out-coot-2.pdb map 5 (#12) relative to cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) coordinates: Matrix rotation and translation 0.99999989 -0.00047232 -0.00003471 0.01200406 0.00047234 0.99999963 0.00072238 -0.20737148 0.00003437 -0.00072239 0.99999974 0.08331265 Axis -0.83629942 -0.03998769 0.54681283 Axis point 0.00000000 82.06384152 284.68493080 Rotation angle (degrees) 0.04949148 Shift along axis 0.04380974 Average map value = 0.5129 for 15253 atoms, 2459 outside contour > ui tool show ""Map Filter"" > volume gaussian #11 sDev 1.1 Opened cryosparc_P5_J968_004_volume_map_sharp_inv.mrc gaussian as #13, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > transparency #13.1 50 > volume #13 level 0.1404 > open /Users/nicholasferraro/Replicase/AMP-PnP-ATP/AMP-PnP- > ATP_Models_Phenix/Rep_F-chain.pdb Rep_F-chain.pdb title: Cryo-em structure of PCV2 replicase bound to ssDNA [more info...] Chain information for Rep_F-chain.pdb #14 --- Chain | Description | UniProt F | atp-dependent helicase rep | Q6TC59_PCV2 1-314 > hide #14 models > show #!12 models > hide #!12 models > close #12 > close #9 > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968-RSR-Regclash-out- > coot-2.pdb Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP- PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968-RSR-Regclash-out- coot-2.pdb --- warnings | Duplicate atom serial number found: 9340 Duplicate atom serial number found: 12880 Duplicate atom serial number found: 13463 Chain information for J968-RSR-Regclash-out-coot-2.pdb #9 --- Chain | Description A B C D E | No description available F | No description available G | No description available Opened J968-RSR-Regclash-out-coot-2.pdb map 5 as #12, grid size 65,70,76, pixel 1.67, shown at level 0.115, step 1, values float32 > fitmap #9 inMap #11 resolution 5 Fit map J968-RSR-Regclash-out-coot-2.pdb map 5 in map cryosparc_P5_J968_004_volume_map_sharp_inv.mrc using 31951 points correlation = 0.8218, correlation about mean = 0.6725, overlap = 5770 steps = 44, shift = 0.0803, angle = 0.0559 degrees Position of J968-RSR-Regclash-out-coot-2.pdb map 5 (#12) relative to cryosparc_P5_J968_004_volume_map_sharp_inv.mrc (#11) coordinates: Matrix rotation and translation 0.99999999 -0.00015335 -0.00007506 -0.02388188 0.00015342 0.99999953 0.00096011 -0.20291118 0.00007491 -0.00096012 0.99999954 0.11236664 Axis -0.98455494 -0.07689316 0.15728641 Axis point 0.00000000 107.63107755 206.84718171 Rotation angle (degrees) 0.05587336 Shift along axis 0.05678925 Average map value = 0.5147 for 15853 atoms, 2515 outside contour > show #14 models > select #14/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > fitmap #14 inMap #13 Fit molecule Rep_F-chain.pdb (#14) to map cryosparc_P5_J968_004_volume_map_sharp_inv.mrc gaussian (#13) using 2301 atoms average map value = 0.2469, steps = 80 shifted from previous position = 4.56 rotated from previous position = 11.8 degrees atoms outside contour = 530, contour level = 0.14036 Position of Rep_F-chain.pdb (#14) relative to cryosparc_P5_J968_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates: Matrix rotation and translation 0.98020244 0.06268018 0.18781474 -28.48538168 -0.07257796 0.99628804 0.04628801 4.07138667 -0.18421624 -0.05900283 0.98111317 34.60542112 Axis -0.25704560 0.90823595 -0.33020450 Axis point 169.68189378 0.00000000 170.11070766 Rotation angle (degrees) 11.81835657 Shift along axis -0.40704422 > hide #!13 models > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968_F-chain_in.pdb > models #14 relModel #9 > show #!12 models > show #!11 models > close #9,11-13 > hide #14 models > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J981_with_FOD/Round_000_real_space_refined_m5_001.pdb Chain information for Round_000_real_space_refined_m5_001.pdb #9 --- Chain | Description A B C D E F | No description available G | No description available > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J981_with_FOD/cryosparc_P5_J981_004_volume_map_sharp_inv.mrc Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc as #11, grid size 300,300,300, pixel 0.844, shown at level 0.187, step 2, values float32 Opened Round_000_real_space_refined_m5_001.pdb map 5 as #12, grid size 73,69,75, pixel 1.67, shown at level 0.116, step 1, values float32 > fitmap #9 inMap #11 resolution 5 Fit map Round_000_real_space_refined_m5_001.pdb map 5 in map cryosparc_P5_J981_004_volume_map_sharp_inv.mrc using 36757 points correlation = 0.7533, correlation about mean = 0.7276, overlap = 7851 steps = 60, shift = 0.0451, angle = 0.00889 degrees Position of Round_000_real_space_refined_m5_001.pdb map 5 (#12) relative to cryosparc_P5_J981_004_volume_map_sharp_inv.mrc (#11) coordinates: Matrix rotation and translation 1.00000000 0.00000938 0.00008330 -0.04567419 -0.00000939 0.99999999 0.00013050 -0.04439060 -0.00008330 -0.00013050 0.99999999 0.02084044 Axis -0.84137711 0.53705038 -0.06050981 Axis point 0.00000000 165.83812057 395.01508720 Rotation angle (degrees) 0.00888684 Shift along axis 0.01332818 Average map value = 0.7111 for 18135 atoms, 2551 outside contour > surface dust #11 size 8.44 > fitmap #9 inMap #11 resolution 5 Fit map Round_000_real_space_refined_m5_001.pdb map 5 in map cryosparc_P5_J981_004_volume_map_sharp_inv.mrc using 36757 points correlation = 0.7533, correlation about mean = 0.7275, overlap = 7851 steps = 44, shift = 0.0162, angle = 0.0139 degrees Position of Round_000_real_space_refined_m5_001.pdb map 5 (#12) relative to cryosparc_P5_J981_004_volume_map_sharp_inv.mrc (#11) coordinates: Matrix rotation and translation 0.99999996 -0.00007697 0.00026666 -0.05894520 0.00007697 1.00000000 -0.00000131 -0.03510633 -0.00026666 0.00000133 0.99999996 0.01245642 Axis 0.00476551 0.96076267 0.27733081 Axis point 78.46177691 0.00000000 220.51661181 Rotation angle (degrees) 0.01590236 Shift along axis -0.03055520 Average map value = 0.7111 for 18135 atoms, 2557 outside contour > ui tool show ""Map Filter"" Window position QRect(954,1009 807x134) outside any known screen, using primary screen > volume gaussian #11 sDev 1.1 Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian as #13, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > volume gaussian #11 sDev 1.16 modelId #13 Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian as #13, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > volume gaussian #11 sDev 0.95 modelId #13 Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian as #13, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > volume gaussian #11 sDev 1.02 modelId #13 Opened cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian as #13, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > select protein 177836 atoms, 180553 bonds, 8 pseudobonds, 11235 residues, 14 models selected > fitmap #9 inMap #13 Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135 atoms average map value = 0.4741, steps = 44 shifted from previous position = 0.0191 rotated from previous position = 0.0385 degrees atoms outside contour = 2855, contour level = 0.19564 Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates: Matrix rotation and translation 0.99999994 -0.00020620 -0.00028703 0.01396351 0.00020630 0.99999991 0.00035738 -0.08792908 0.00028696 -0.00035744 0.99999989 -0.00958410 Axis -0.71106260 -0.57097381 0.41033996 Axis point 0.00000000 -68.59145060 187.95862302 Rotation angle (degrees) 0.02879897 Shift along axis 0.03634354 > fitmap #9 inMap #13 Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135 atoms average map value = 0.4741, steps = 44 shifted from previous position = 0.013 rotated from previous position = 0.0117 degrees atoms outside contour = 2847, contour level = 0.19564 Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates: Matrix rotation and translation 0.99999997 -0.00020659 -0.00012645 0.00160601 0.00020662 0.99999995 0.00023118 -0.08004404 0.00012640 -0.00023120 0.99999997 -0.01048149 Axis -0.69045057 -0.37756311 0.61702844 Axis point 0.00000000 -105.81681497 309.23968334 Rotation angle (degrees) 0.01918482 Shift along axis 0.02264543 > fitmap #9 inMap #13 Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135 atoms average map value = 0.4741, steps = 44 shifted from previous position = 0.00852 rotated from previous position = 0.00996 degrees atoms outside contour = 2852, contour level = 0.19564 Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates: Matrix rotation and translation 0.99999996 -0.00026473 0.00002971 -0.01301395 0.00026473 0.99999995 0.00018158 -0.07654306 -0.00002976 -0.00018157 0.99999998 -0.00260143 Axis -0.56321959 0.09223704 0.82114312 Axis point 288.47831851 -53.16852251 0.00000000 Rotation angle (degrees) 0.01847172 Shift along axis -0.00186653 > fitmap #9 inMap #13 Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135 atoms average map value = 0.4741, steps = 44 shifted from previous position = 0.0148 rotated from previous position = 0.0105 degrees atoms outside contour = 2846, contour level = 0.19564 Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates: Matrix rotation and translation 0.99999998 -0.00015172 -0.00011330 -0.00693700 0.00015175 0.99999997 0.00020271 -0.07132349 0.00011327 -0.00020272 0.99999997 -0.00634114 Axis -0.73076374 -0.40839385 0.54699069 Axis point 0.00000000 -114.23166267 289.92981066 Rotation angle (degrees) 0.01589387 Shift along axis 0.03072884 > fitmap #9 inMap #13 Fit molecule Round_000_real_space_refined_m5_001.pdb (#9) to map cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) using 18135 atoms average map value = 0.4741, steps = 44 shifted from previous position = 0.00758 rotated from previous position = 0.00383 degrees atoms outside contour = 2847, contour level = 0.19564 Position of Round_000_real_space_refined_m5_001.pdb (#9) relative to cryosparc_P5_J981_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates: Matrix rotation and translation 0.99999997 -0.00020319 -0.00013563 0.00239800 0.00020322 0.99999995 0.00023892 -0.08048452 0.00013558 -0.00023895 0.99999996 -0.01177430 Axis -0.69922219 -0.39683366 0.59465232 Axis point 0.00000000 -107.20814946 298.20661583 Rotation angle (degrees) 0.01957906 Shift along axis 0.02326062 > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J981_with_FOD/J981_F- > chain.pdb models #9 relModel #11 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #13 > close #12 > close #9 > close #11 > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J983/Round_001_J983_with_FOD_real_space_refined_m4_001.pdb Chain information for Round_001_J983_with_FOD_real_space_refined_m4_001.pdb #9 --- Chain | Description A | No description available B C D E | No description available F | No description available G | No description available > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J983/cryosparc_P5_J983_006_volume_map_sharp_inv.mrc Opened cryosparc_P5_J983_006_volume_map_sharp_inv.mrc as #11, grid size 300,300,300, pixel 0.844, shown at level 0.181, step 2, values float32 > surface dust #11 size 8.44 > volume gaussian #11 sDev 1.02 Opened cryosparc_P5_J983_006_volume_map_sharp_inv.mrc gaussian as #12, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > volume gaussian #11 sDev 1.09 modelId #12 Opened cryosparc_P5_J983_006_volume_map_sharp_inv.mrc gaussian as #12, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > transparency #12.1 50 > show #14 models > select #14/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > fitmap #14 inMap #12 Fit molecule Rep_F-chain.pdb (#14) to map cryosparc_P5_J983_006_volume_map_sharp_inv.mrc gaussian (#12) using 2301 atoms average map value = 0.2597, steps = 52 shifted from previous position = 1.77 rotated from previous position = 3.69 degrees atoms outside contour = 753, contour level = 0.18978 Position of Rep_F-chain.pdb (#14) relative to cryosparc_P5_J983_006_volume_map_sharp_inv.mrc gaussian (#12) coordinates: Matrix rotation and translation 0.98620852 0.00495050 0.16543353 -19.12819427 -0.01182260 0.99910630 0.04058109 -3.82838013 -0.16508478 -0.04197727 0.98538567 29.67738027 Axis -0.24204566 0.96901788 -0.04917560 Axis point 168.06391931 0.00000000 130.42443323 Rotation angle (degrees) 9.81938803 Shift along axis -0.53927530 > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J983/J983_F- > chain_fit.pdb models #14 relModel #9 > close #9,11-12 > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J985/Phenix/Round_000_real_space_refined_m6_001_with_FOD.pdb Summary of feedback from opening /Users/nicholasferraro/Replicase/AMP- PnP/ssDNA/J985/Phenix/Round_000_real_space_refined_m6_001_with_FOD.pdb --- warning | Cannot find LINK/SSBOND residue ARG (232 ) Chain information for Round_000_real_space_refined_m6_001_with_FOD.pdb #9 --- Chain | Description A B C D E | No description available F | No description available G | No description available > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J985/cryosparc_P5_J985_004_volume_map_sharp_inv.mrc Opened cryosparc_P5_J985_004_volume_map_sharp_inv.mrc as #11, grid size 300,300,300, pixel 0.844, shown at level 0.175, step 2, values float32 > surface dust #11 size 8.44 Opened Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 as #12, grid size 68,69,77, pixel 1.67, shown at level 0.115, step 1, values float32 > fitmap #9 inMap #11 resolution 5 Fit map Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 in map cryosparc_P5_J985_004_volume_map_sharp_inv.mrc using 31939 points correlation = 0.8776, correlation about mean = 0.7267, overlap = 6126 steps = 40, shift = 0.0315, angle = 0.0772 degrees Position of Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 (#12) relative to cryosparc_P5_J985_004_volume_map_sharp_inv.mrc (#11) coordinates: Matrix rotation and translation 0.99999917 0.00090400 0.00091545 -0.24954701 -0.00090436 0.99999951 0.00040005 0.04446861 -0.00091509 -0.00040087 0.99999950 0.15237744 Axis -0.29719846 0.67925838 -0.67102990 Axis point 167.92359338 0.00000000 272.05824455 Rotation angle (degrees) 0.07720340 Shift along axis 0.00212085 Average map value = 0.5315 for 15766 atoms, 1934 outside contour > fitmap #9 inMap #11 resolution 5 Fit map Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 in map cryosparc_P5_J985_004_volume_map_sharp_inv.mrc using 31939 points correlation = 0.8776, correlation about mean = 0.7266, overlap = 6126 steps = 48, shift = 0.0131, angle = 0.0099 degrees Position of Round_000_real_space_refined_m6_001_with_FOD.pdb map 5 (#12) relative to cryosparc_P5_J985_004_volume_map_sharp_inv.mrc (#11) coordinates: Matrix rotation and translation 0.99999924 0.00092810 0.00080995 -0.24170122 -0.00092853 0.99999943 0.00053479 0.03031724 -0.00080945 -0.00053555 0.99999953 0.16947538 Axis -0.39847339 0.60288161 -0.69119659 Axis point 34.14579185 261.55015794 0.00000000 Rotation angle (degrees) 0.07695128 Shift along axis -0.00255159 Average map value = 0.5315 for 15766 atoms, 1944 outside contour The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume gaussian #11 sDev 1.09 Opened cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian as #13, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > volume gaussian #11 sDev 1.19 modelId #13 Opened cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian as #13, grid size 300,300,300, pixel 0.844, shown at step 1, values float32 > select #14/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > fitmap #14 inMap #13 Fit molecule Rep_F-chain.pdb (#14) to map cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian (#13) using 2301 atoms average map value = 0.2611, steps = 88 shifted from previous position = 7.75 rotated from previous position = 14.7 degrees atoms outside contour = 682, contour level = 0.18452 Position of Rep_F-chain.pdb (#14) relative to cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates: Matrix rotation and translation 0.99359813 -0.10944935 -0.02799292 21.44980875 0.10713511 0.99149326 -0.07391332 -3.06923684 0.03584456 0.07044111 0.99687172 -12.21693772 Axis 0.53864251 -0.23820244 0.80816078 Axis point 37.72983201 181.90388082 0.00000000 Rotation angle (degrees) 7.70070461 Shift along axis 2.41162853 > transparency #13.1 50 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J985/J985_F- > chain_fit.pdb models #14 relModel #9 > hide #!11 models > select #14/F 2301 atoms, 2341 bonds, 144 residues, 1 model selected > fitmap #14 inMap #13 Fit molecule Rep_F-chain.pdb (#14) to map cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian (#13) using 2301 atoms average map value = 0.2611, steps = 40 shifted from previous position = 0.00972 rotated from previous position = 0.0105 degrees atoms outside contour = 683, contour level = 0.18452 Position of Rep_F-chain.pdb (#14) relative to cryosparc_P5_J985_004_volume_map_sharp_inv.mrc gaussian (#13) coordinates: Matrix rotation and translation 0.99361681 -0.10930159 -0.02790687 21.42339856 0.10699614 0.99151328 -0.07384602 -3.06644058 0.03574152 0.07038872 0.99687912 -12.19650890 Axis 0.53888196 -0.23779967 0.80811976 Axis point 37.71253902 181.88069652 0.00000000 Rotation angle (degrees) 7.69084086 Shift along axis 2.41764162 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #12 > close #11,13 > close #14 > close #9 > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968_F-chain_in.pdb J968_F-chain_in.pdb title: Cryo-em structure of PCV2 replicase bound to ssDNA [more info...] Chain information for J968_F-chain_in.pdb #9 --- Chain | Description | UniProt F | atp-dependent helicase rep | Q6TC59_PCV2 1-314 > open /Users/nicholasferraro/Replicase/AMP- > PnP/ssDNA/J968_with_FOD/Phenix/Round_001/Round_002/J968_F-chain.pdb Chain information for J968_F-chain.pdb #11 --- Chain | Description A B C D E | No description available F | No description available G | No description available > hide #!11 models > close #9 > show #!11 models > open /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J981_with_FOD/J981_F- > chain.pdb Chain information for J981_F-chain.pdb #9 --- Chain | Description A B C D E F | No description available G | No description available > hide #!11 models > select #9/F 2964 atoms, 3014 bonds, 1 pseudobond, 185 residues, 2 models selected > select clear > hide #!9 models > open /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J983/J983_with_F- > chain.pdb Chain information for J983_with_F-chain.pdb #12 --- Chain | Description A | No description available B C D E | No description available F | No description available G | No description available > open /Users/nicholasferraro/Replicase/AMP-PnP/ssDNA/J985/J985_with_F- > chain.pdb Chain information for J985_with_F-chain.pdb #13 --- Chain | Description A B C D E | No description available F | No description available G | No description available > show #!9 models > show #!11 models > select #1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A 38676 atoms, 39283 bonds, 11 pseudobonds, 2427 residues, 24 models selected > color (#!9,11-13 & sel) #ff85ffff > select #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B 38655 atoms, 39255 bonds, 11 pseudobonds, 2426 residues, 23 models selected > color (#!9,11-13 & sel) #73fa79ff > select #1/C#2/C#3/C#4/C#5/C#6/C#7/C#8/C#9/C#10/C#11/C#12/C#13/C 38654 atoms, 39260 bonds, 9 pseudobonds, 2426 residues, 21 models selected > color (#!9,11-13 & sel) #fffc79ff > color (#!9,11-13 & sel) #7a81ffff > select #1/D#2/D#3/D#4/D#5/D#6/D#7/D#8/D#9/D#10/D#11/D#12/D#13/D 38790 atoms, 39414 bonds, 7 pseudobonds, 2435 residues, 19 models selected > color (#!9,11-13 & sel) #76d6ffff > select #1/E#2/E#3/E#4/E#5/E#6/E#7/E#8/E#9/E#10/E#11/E#12/E#13/E 38530 atoms, 39145 bonds, 3 pseudobonds, 2413 residues, 16 models selected > color (#!9,11-13 & sel) #fffc79ff > select #1/F#2/F#3/F#4/F#5/F#6/F#7/F#8/F#9/F#10/F#11/F#12/F#13/F 37674 atoms, 38238 bonds, 3 pseudobonds, 2381 residues, 16 models selected > color (#!9,11-13 & sel) #ff7e79ff > select clear > select ligand 4457 atoms, 4694 bonds, 126 residues, 13 models selected > color (#!9,11-13 & sel) dim gray > color sel & #!9,11-13 byhetero > select clear > select protein 228689 atoms, 232243 bonds, 25 pseudobonds, 14411 residues, 19 models selected > style sel & #!9,11-13 ball Changed 70948 atom styles > show sel & #!9,11-13 cartoons > hide sel & #!9,11-13 atoms > select clear > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!9 models > hide #!12 models > hide #!13 models > hide #!11 models > show #!11 models > show #!9 models > hide #!11 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!13 models > hide #!9 models > show #!9 models > show #!12 models > show #!11 models > hide #!11 models > hide #!9 models > hide #!12 models > show #!12 models > show #!11 models > show #!9 models > hide #!9 models > hide #!11 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!12 models > show #!9 models > show #!12 models > hide #!12 models > show #!12 models > show #!11 models > hide #!11 models > hide #!12 models > hide #!9 models > show #!12 models > hide #!12 models > show #!9 models > show #!12 models > show #!11 models > morph #13,9,12,11 frames 10 Computed 31 frame morph #14 > coordset #14 1,31 > movie record > movie encode /Users/nicholasferraro/Desktop/movie8.mp4 framerate 25.0 Movie saved to /Users/nicholasferraro/Desktop/movie8.mp4 > morph #13,9,12,11 frames 25 Computed 76 frame morph #15 > coordset #15 1,76 > close #14-15 > show #!13 models > show #!12 models > show #!11 models > show #!9 models > matchmaker #9/C to #13/C pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker J985_with_F-chain.pdb, chain C (#13) with J981_F-chain.pdb, chain C (#9), sequence alignment score = 949.9 RMSD between 185 pruned atom pairs is 0.307 angstroms; (across all 185 pairs: 0.307) > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #11/C to #13/C pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker J985_with_F-chain.pdb, chain C (#13) with J968_F-chain.pdb, chain C (#11), sequence alignment score = 955.9 RMSD between 185 pruned atom pairs is 0.473 angstroms; (across all 185 pairs: 0.473) > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #12/C to #13/C pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker J985_with_F-chain.pdb, chain C (#13) with J983_with_F-chain.pdb, chain C (#12), sequence alignment score = 959.1 RMSD between 184 pruned atom pairs is 0.332 angstroms; (across all 184 pairs: 0.332) > morph #13,9,12,11 frames 25 Computed 76 frame morph #14 > coordset #14 1,76 > movie record > movie encode /Users/nicholasferraro/Desktop/movie8.mp4 framerate 25.0 Error processing trigger ""new frame"": Movie encoding failed because no images were recorded. > movie record > movie encode /Users/nicholasferraro/Desktop/movie8.mp4 framerate 25.0 Movie saved to /Users/nicholasferraro/Desktop/movie8.mp4 > hide #!14 models > open > /Users/nicholasferraro/Desktop/fold_2024_08_12_15_49/fold_2024_08_12_15_49_full_data_0.json Traceback (most recent call last): File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/dialog.py"", line 334, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/__init__.py"", line 129, in open structs = [m for m in session.models.list(type = AtomicStructure) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/k8/_w4jc1fn05qcb4fz7n3bs2b40000gn/T/AppTranslocation/CCDCC6C4-7682-4DD2-B515-8761D86DEC85/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/__init__.py"", line 130, in if hasattr(m, 'filename') and dirname(m.filename) == dirname(path)] ^^^^^^^^^^^^^^^^^^^ File """", line 152, in dirname TypeError: expected str, bytes or os.PathLike object, not NoneType TypeError: expected str, bytes or os.PathLike object, not NoneType File """", line 152, in dirname See log for complete Python traceback. > show #!13 models > show #!12 models > show #!11 models > show #!9 models > hide #!11 models > hide #!12 models > show #!12 models > hide #!13 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!12 models > show #!11 models > show #!12 models > show #!13 models > morph #13,9,12,11 frames 4 Computed 13 frame morph #15 > coordset #15 1,13 > hide #!15 models > show #!13 models > show #!12 models > hide #!13 models > show #!13 models > hide #!12 models > show #!12 models > hide #!12 models > show #!11 models > hide #!13 models > show #!9 models > hide #!11 models > show #!11 models > hide #!9 models > show #!10 models > hide #!10 models > show #!13 models > hide #!11 models > hide #!13 models > show #!12 models Cell requested for row 11 is out of bounds for table with 17 rows! Resizing table model. > close #9,11-13 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: MK1A3LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 4 days, 20 hours, 53 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate Eric Pettersen all ChimeraX