id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19508 Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.1-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x00000001ef576080 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File 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All rights reserved. How to cite UCSF ChimeraX > open 7rdy format mmcif fromDatabase pdb 7rdy title: SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - engaged class [more info...] Chain information for 7rdy #1 --- Chain | Description | UniProt A | RNA-directed RNA polymerase | R1AB_SARS2 1-932 B D | Non-structural protein 8 | R1AB_SARS2 1-198 C | Non-structural protein 7 | R1AB_SARS2 1-83 E F | Helicase | R1AB_SARS2 1-601 P | Product RNA | T | Template RNA | Non-standard residues in 7rdy #1 --- 1N7 — chapso (2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium) ADP — adenosine-5'-diphosphate AF3 — aluminum fluoride MG — magnesium ion ZN — zinc ion > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select /A 7597 atoms, 7794 bonds, 13 pseudobonds, 934 residues, 2 models selected > color sel light slate gray > select /P 719 atoms, 802 bonds, 34 residues, 1 model selected > color sel burnt brick Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > ui tool show ""Color Actions"" > color sel fire brick > select /T 934 atoms, 1042 bonds, 1 pseudobond, 44 residues, 2 models selected > color sel sky blue > select B Nothing selected > select /B 1408 atoms, 1427 bonds, 186 residues, 1 model selected > color sel dark green > select /D 1415 atoms, 1434 bonds, 185 residues, 1 model selected > color sel forrest green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel forest green > select /E 4605 atoms, 4706 bonds, 15 pseudobonds, 596 residues, 2 models selected > color sel salmon > select /F 4592 atoms, 4691 bonds, 14 pseudobonds, 596 residues, 2 models selected > color sel dark salmon > sel/C Unknown command: sel/C > select /C 576 atoms, 579 bonds, 75 residues, 1 model selected > color sel gold > hide atoms > show cartoons > save ""/Users/nathansoper/Google Drive/My Drive/Lab - Tania/6th year > meetings/Figures/holo-RdRp.cxs"" > open 7d4f 7d4f title: Structure of COVID-19 RNA-dependent RNA polymerase bound to suramin [more info...] Chain information for 7d4f #2 --- Chain | Description | UniProt A | RNA-directed RNA polymerase | R1AB_SARS2 1-932 B G | Non-structural protein 8 | R1AB_SARS2 1-198 C | Non-structural protein 7 | R1AB_SARS2 1-83 Non-standard residues in 7d4f #2 --- H3U — 8-(3-(3-aminobenzamido)-4-methylbenzamido)naphthalene-1,3,5-trisulfonic acid ZN — zinc ion > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7rdy, chain A (#1) with 7d4f, chain A (#2), sequence alignment score = 4588.5 RMSD between 872 pruned atom pairs is 0.542 angstroms; (across all 898 pairs: 1.022) > select #2 9534 atoms, 9750 bonds, 11 pseudobonds, 1185 residues, 4 models selected > ~select #2:H3U 9450 atoms, 9660 bonds, 11 pseudobonds, 1183 residues, 4 models selected > delete sel > select H3U Expected an objects specifier or a keyword > select #2 84 atoms, 90 bonds, 2 residues, 1 model selected > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... Errors may have occurred when running pip: pip standard error: \--- ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. nptyping 2.5.0 requires numpy=1.20.0; python_version >= ""3.8"", but you have numpy 2.3.5 which is incompatible. scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.3.5 which is incompatible. \--- pip standard output: \--- \--- pyKVFinder module installed from PyPi repository. > kvfinder #1 159 cavities found for 7rdy #1 7rdy Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.4.9 | | 2626.56 | 1705.07 | 12160 | 15.3 | 3.59 1.4.94 | | 1259.06 | 1138.87 | 5829 | 21.75 | 8.01 1.4.151 | | 1024.06 | 626.78 | 4741 | 5.47 | 1.55 1.4.116 | | 881.5 | 606.73 | 4081 | 7 | 2.49 1.4.24 | | 555.34 | 535.81 | 2571 | 14.26 | 4.74 1.4.125 | | 551.23 | 390.15 | 2552 | 5.13 | 1.35 1.4.132 | | 444.96 | 306.07 | 2060 | 6.84 | 1.94 1.4.100 | | 443.45 | 414.84 | 2053 | 0 | 0 1.4.57 | | 428.98 | 471.54 | 1986 | 9.84 | 2.6 1.4.81 | | 392.47 | 357.18 | 1817 | 4.8 | 1.46 1.4.149 | | 369.79 | 357.15 | 1712 | 13.2 | 4.19 1.4.84 | | 246.02 | 248.59 | 1139 | 8.14 | 3.09 1.4.102 | | 245.81 | 240.17 | 1138 | 7.25 | 2.38 1.4.32 | | 243 | 228.71 | 1125 | 8.07 | 3.36 1.4.108 | | 240.41 | 243.38 | 1113 | 5.91 | 1.49 1.4.12 | | 232.85 | 268.9 | 1078 | 0 | 0 1.4.127 | | 228.31 | 173.22 | 1057 | 4.24 | 1.44 1.4.96 | | 223.78 | 255.74 | 1036 | 4.69 | 1.56 1.4.95 | | 223.56 | 230.6 | 1035 | 6.71 | 2.9 1.4.117 | | 216.65 | 238.64 | 1003 | 9.66 | 2.58 1.4.62 | | 207.14 | 248.87 | 959 | 9.56 | 3.51 1.4.52 | | 193.32 | 194.01 | 895 | 6.71 | 3.09 1.4.42 | | 178.2 | 197.45 | 825 | 7.78 | 2.42 1.4.99 | | 153.14 | 196.52 | 709 | 4.87 | 1.48 1.4.51 | | 149.04 | 100.32 | 690 | 3.29 | 0.9 1.4.122 | | 146.23 | 150.69 | 677 | 0 | 0 1.4.126 | | 141.91 | 118.99 | 657 | 3.23 | 0.87 1.4.17 | | 134.78 | 127.21 | 624 | 2.62 | 0.73 1.4.78 | | 132.19 | 177.34 | 612 | 7.68 | 2.63 1.4.154 | | 123.12 | 122.54 | 570 | 3.06 | 1 1.4.73 | | 115.78 | 121.71 | 536 | 4.87 | 1.53 1.4.64 | | 111.89 | 161.25 | 518 | 4.72 | 1.33 1.4.50 | | 108.86 | 120.71 | 504 | 4.24 | 1.25 1.4.77 | | 92.23 | 63.75 | 427 | 1.47 | 0.35 1.4.115 | | 92.23 | 98.69 | 427 | 4.28 | 1.23 1.4.88 | | 91.58 | 116.03 | 424 | 0 | 0 1.4.20 | | 87.26 | 101.76 | 404 | 0 | 0 1.4.113 | | 86.83 | 96.4 | 402 | 3.84 | 1.48 1.4.114 | | 80.78 | 84.32 | 374 | 2.47 | 0.68 1.4.18 | | 73.66 | 97.24 | 341 | 0 | 0 1.4.105 | | 71.28 | 65.91 | 330 | 1.9 | 0.39 1.4.134 | | 70.85 | 104.36 | 328 | 2.55 | 0.71 1.4.118 | | 70.63 | 83.24 | 327 | 2.62 | 0.85 1.4.136 | | 63.29 | 66.02 | 293 | 3 | 1.12 1.4.8 | | 59.83 | 82.91 | 277 | 2.94 | 0.95 1.4.45 | | 57.89 | 71.97 | 268 | 4.02 | 1.4 1.4.3 | | 57.46 | 78.9 | 266 | 0 | 0 1.4.130 | | 57.24 | 82.91 | 265 | 5.2 | 2.43 1.4.157 | | 54.86 | 67.85 | 254 | 3.23 | 1.22 1.4.69 | | 51.41 | 70.74 | 238 | 0 | 0 1.4.22 | | 49.03 | 52.23 | 227 | 2.47 | 0.88 1.4.46 | | 49.03 | 46.68 | 227 | 2.4 | 0.69 1.4.38 | | 48.17 | 84.06 | 223 | 0 | 0 1.4.139 | | 48.17 | 68.42 | 223 | 4.02 | 1.74 1.4.140 | | 48.17 | 54.4 | 223 | 3 | 0.88 1.4.145 | | 45.79 | 70.16 | 212 | 1.8 | 0.68 1.4.44 | | 44.71 | 54.41 | 207 | 1.7 | 0.59 1.4.30 | | 42.77 | 50.41 | 198 | 1.9 | 0.67 1.4.72 | | 42.55 | 57.97 | 197 | 3.29 | 1.21 1.4.14 | | 42.34 | 66.92 | 196 | 0 | 0 1.4.23 | | 41.26 | 73.64 | 191 | 0 | 0 1.4.107 | | 40.61 | 54.09 | 188 | 3.65 | 1.13 1.4.138 | | 40.61 | 60.75 | 188 | 5.2 | 2.29 1.4.131 | | 39.31 | 51.21 | 182 | 3.65 | 1.41 1.4.29 | | 37.15 | 58.6 | 172 | 2.47 | 0.74 1.4.156 | | 36.07 | 47.27 | 167 | 2.47 | 0.94 1.4.53 | | 34.78 | 51.76 | 161 | 1.2 | 0.24 1.4.85 | | 34.34 | 45.34 | 159 | 3.23 | 1.38 1.4.159 | | 34.13 | 43.97 | 158 | 1.9 | 0.63 1.4.25 | | 33.48 | 43.28 | 155 | 1.34 | 0.4 1.4.65 | | 32.4 | 47.59 | 150 | 3 | 0.83 1.4.83 | | 32.4 | 54.44 | 150 | 0 | 0 1.4.13 | | 32.18 | 51.64 | 149 | 0 | 0 1.4.26 | | 32.18 | 44.02 | 149 | 1.2 | 0.29 1.4.90 | | 30.89 | 43.49 | 143 | 1.8 | 0.59 1.4.103 | | 30.89 | 47.51 | 143 | 1.7 | 0.5 1.4.37 | | 30.46 | 46.79 | 141 | 1.7 | 0.53 1.4.48 | | 30.02 | 59.94 | 139 | 3.7 | 1.41 1.4.68 | | 30.02 | 45.23 | 139 | 1.34 | 0.39 1.4.106 | | 29.81 | 50.49 | 138 | 3.84 | 1.92 1.4.11 | | 29.16 | 46.36 | 135 | 2.47 | 0.71 1.4.19 | | 29.16 | 41.75 | 135 | 1.7 | 0.34 1.4.89 | | 29.16 | 52.8 | 135 | 0 | 0 1.4.133 | | 29.16 | 43.63 | 135 | 1.34 | 0.43 1.4.49 | | 28.3 | 55.43 | 131 | 0 | 0 1.4.91 | | 28.3 | 46.14 | 131 | 0 | 0 1.4.36 | | 27.65 | 41.39 | 128 | 1.8 | 0.46 1.4.59 | | 27.43 | 53.74 | 127 | 0 | 0 1.4.5 | | 26.57 | 41.47 | 123 | 2.94 | 1.6 1.4.31 | | 26.57 | 36.9 | 123 | 1.34 | 0.34 1.4.21 | | 26.14 | 43.12 | 121 | 3.23 | 1.55 1.4.35 | | 26.14 | 46.24 | 121 | 0 | 0 1.4.111 | | 26.14 | 46.8 | 121 | 0 | 0 1.4.86 | | 25.27 | 43.38 | 117 | 0 | 0 1.4.120 | | 25.06 | 35.43 | 116 | 1.34 | 0.32 1.4.121 | | 24.62 | 38.5 | 114 | 2.62 | 1.45 1.4.143 | | 24.62 | 57.97 | 114 | 0 | 0 1.4.82 | | 24.19 | 33.83 | 112 | 2.08 | 0.75 1.4.158 | | 22.9 | 39.53 | 106 | 0.85 | 0.2 1.4.28 | | 22.68 | 35.36 | 105 | 2.24 | 0.88 1.4.75 | | 22.68 | 32.14 | 105 | 1.8 | 0.5 1.4.60 | | 22.25 | 36.32 | 103 | 1.2 | 0.24 1.4.4 | | 21.6 | 35.38 | 100 | 1.34 | 0.42 1.4.43 | | 20.74 | 41.19 | 96 | 0 | 0 1.4.141 | | 20.74 | 33.96 | 96 | 2.16 | 0.87 1.4.7 | | 20.52 | 36.4 | 95 | 0.85 | 0.19 1.4.16 | | 18.79 | 27.92 | 87 | 1.8 | 0.51 1.4.104 | | 18.79 | 20.06 | 87 | 0.85 | 0.23 1.4.137 | | 18.36 | 23.56 | 85 | 1.34 | 0.5 1.4.34 | | 17.5 | 25.82 | 81 | 1.8 | 0.5 1.4.41 | | 17.5 | 30.46 | 81 | 1.7 | 0.65 1.4.61 | | 17.28 | 25.41 | 80 | 1.2 | 0.32 1.4.80 | | 17.28 | 36.68 | 80 | 0 | 0 1.4.93 | | 17.28 | 36.68 | 80 | 0 | 0 1.4.97 | | 17.28 | 36.68 | 80 | 0 | 0 1.4.128 | | 17.28 | 21.6 | 80 | 0.85 | 0.26 1.4.2 | | 17.06 | 35.72 | 79 | 2.75 | 1.55 1.4.15 | | 16.85 | 32.3 | 78 | 0 | 0 1.4.39 | | 16.85 | 32.3 | 78 | 0 | 0 1.4.110 | | 14.69 | 21.77 | 68 | 1.2 | 0.3 1.4.152 | | 14.69 | 23 | 68 | 0.85 | 0.22 1.4.56 | | 14.26 | 25.14 | 66 | 1.99 | 0.85 1.4.70 | | 13.18 | 19.03 | 61 | 1.34 | 0.39 1.4.6 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.33 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.54 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.76 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.79 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.98 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.112 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.123 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.129 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.135 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.144 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.147 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.155 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.109 | | 12.1 | 17.87 | 56 | 1.34 | 0.46 1.4.58 | | 11.66 | 22.28 | 54 | 1.47 | 0.59 1.4.148 | | 11.66 | 21.35 | 54 | 0.6 | 0.18 1.4.153 | | 11.45 | 20.68 | 53 | 1.34 | 0.52 1.4.92 | | 11.02 | 20.98 | 51 | 0.85 | 0.34 1.4.124 | | 10.58 | 19.41 | 49 | 0.85 | 0.21 1.4.71 | | 9.72 | 18 | 45 | 1.34 | 0.54 1.4.27 | | 9.29 | 15.54 | 43 | 0.6 | 0.11 1.4.47 | | 8.86 | 18.26 | 41 | 1.34 | 0.46 1.4.40 | | 8.42 | 19.26 | 39 | 1.2 | 0.48 1.4.142 | | 7.78 | 14.22 | 36 | 0.6 | 0.2 1.4.87 | | 7.34 | 13.01 | 34 | 1.2 | 0.32 1.4.146 | | 7.34 | 15.4 | 34 | 0.85 | 0.28 1.4.150 | | 7.34 | 17.59 | 34 | 1.2 | 0.41 1.4.10 | | 6.91 | 12.61 | 32 | 0.85 | 0.25 1.4.119 | | 6.91 | 13.51 | 32 | 0.85 | 0.18 1.4.74 | | 6.05 | 9.31 | 28 | 0.6 | 0.15 1.4.66 | | 5.83 | 12.01 | 27 | 0.85 | 0.33 1.4.1 | | 5.62 | 11.34 | 26 | 0.6 | 0.18 1.4.67 | | 5.62 | 11.34 | 26 | 0.6 | 0.18 1.4.55 | | 5.18 | 7.82 | 24 | 0.6 | 0.1 1.4.63 | | 5.18 | 11.37 | 24 | 0.85 | 0.24 1.4.101 | | 5.18 | 12.01 | 24 | 0.6 | 0.12 Populating font family aliases took 116 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > view #1.4.9 @ zoom 0.75 moved plane near -65.08717597850756 [ 0.86425838 -0.25540003 -0.4333916 ] moved plane far -65.08717597850756 [ 0.86425838 -0.25540003 -0.4333916 ] > surface #1.4.1-159 transparency 50 > ~surface #1.4 > surface #1.4.9 > show > #!1/F:114,120,123-124,131-132,134-135,138-139,142-143,145-147,149,165,167,173-181,200-203,206-209,227-236,309-312,335,337-340,342,359-362,378-383,385-386,389-390,405-410,417,421-423,484,486,488,490,514-517,519-521,523-524,530-537,560 > view #!1.4.94 @ zoom 0.75 moved plane near -59.30354653828738 [ 0.86425838 -0.25540003 -0.4333916 ] moved plane far -59.30354653828738 [ 0.86425838 -0.25540003 -0.4333916 ] > ~surface #1.4 > surface #!1.4.94 > show > #!1/E:114,120,123-124,131,134-135,138-139,142-143,145-146,149,173-175,177-181,197-199,212-214,227-228,230,309-311,334-335,337-340,342,360-361,378-383,407-411,417,421-423,484-485/T:7-11 > view #1 > undo Undo failed, probably because structures have been modified. > select #1/A 7597 atoms, 7794 bonds, 13 pseudobonds, 934 residues, 2 models selected > ui tool show ""Find Cavities"" > kvfinder #1 159 cavities found for 7rdy #1 7rdy Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.4.9 | | 2626.56 | 1705.07 | 12160 | 15.3 | 3.59 1.4.94 | | 1259.06 | 1138.87 | 5829 | 21.75 | 8.01 1.4.151 | | 1024.06 | 626.78 | 4741 | 5.47 | 1.55 1.4.116 | | 881.5 | 606.73 | 4081 | 7 | 2.49 1.4.24 | | 555.34 | 535.81 | 2571 | 14.26 | 4.74 1.4.125 | | 551.23 | 390.15 | 2552 | 5.13 | 1.35 1.4.132 | | 444.96 | 306.07 | 2060 | 6.84 | 1.94 1.4.100 | | 443.45 | 414.84 | 2053 | 0 | 0 1.4.57 | | 428.98 | 471.54 | 1986 | 9.84 | 2.6 1.4.81 | | 392.47 | 357.18 | 1817 | 4.8 | 1.46 1.4.149 | | 369.79 | 357.15 | 1712 | 13.2 | 4.19 1.4.84 | | 246.02 | 248.59 | 1139 | 8.14 | 3.09 1.4.102 | | 245.81 | 240.17 | 1138 | 7.25 | 2.38 1.4.32 | | 243 | 228.71 | 1125 | 8.07 | 3.36 1.4.108 | | 240.41 | 243.38 | 1113 | 5.91 | 1.49 1.4.12 | | 232.85 | 268.9 | 1078 | 0 | 0 1.4.127 | | 228.31 | 173.22 | 1057 | 4.24 | 1.44 1.4.96 | | 223.78 | 255.74 | 1036 | 4.69 | 1.56 1.4.95 | | 223.56 | 230.6 | 1035 | 6.71 | 2.9 1.4.117 | | 216.65 | 238.64 | 1003 | 9.66 | 2.58 1.4.62 | | 207.14 | 248.87 | 959 | 9.56 | 3.51 1.4.52 | | 193.32 | 194.01 | 895 | 6.71 | 3.09 1.4.42 | | 178.2 | 197.45 | 825 | 7.78 | 2.42 1.4.99 | | 153.14 | 196.52 | 709 | 4.87 | 1.48 1.4.51 | | 149.04 | 100.32 | 690 | 3.29 | 0.9 1.4.122 | | 146.23 | 150.69 | 677 | 0 | 0 1.4.126 | | 141.91 | 118.99 | 657 | 3.23 | 0.87 1.4.17 | | 134.78 | 127.21 | 624 | 2.62 | 0.73 1.4.78 | | 132.19 | 177.34 | 612 | 7.68 | 2.63 1.4.154 | | 123.12 | 122.54 | 570 | 3.06 | 1 1.4.73 | | 115.78 | 121.71 | 536 | 4.87 | 1.53 1.4.64 | | 111.89 | 161.25 | 518 | 4.72 | 1.33 1.4.50 | | 108.86 | 120.71 | 504 | 4.24 | 1.25 1.4.77 | | 92.23 | 63.75 | 427 | 1.47 | 0.35 1.4.115 | | 92.23 | 98.69 | 427 | 4.28 | 1.23 1.4.88 | | 91.58 | 116.03 | 424 | 0 | 0 1.4.20 | | 87.26 | 101.76 | 404 | 0 | 0 1.4.113 | | 86.83 | 96.4 | 402 | 3.84 | 1.48 1.4.114 | | 80.78 | 84.32 | 374 | 2.47 | 0.68 1.4.18 | | 73.66 | 97.24 | 341 | 0 | 0 1.4.105 | | 71.28 | 65.91 | 330 | 1.9 | 0.39 1.4.134 | | 70.85 | 104.36 | 328 | 2.55 | 0.71 1.4.118 | | 70.63 | 83.24 | 327 | 2.62 | 0.85 1.4.136 | | 63.29 | 66.02 | 293 | 3 | 1.12 1.4.8 | | 59.83 | 82.91 | 277 | 2.94 | 0.95 1.4.45 | | 57.89 | 71.97 | 268 | 4.02 | 1.4 1.4.3 | | 57.46 | 78.9 | 266 | 0 | 0 1.4.130 | | 57.24 | 82.91 | 265 | 5.2 | 2.43 1.4.157 | | 54.86 | 67.85 | 254 | 3.23 | 1.22 1.4.69 | | 51.41 | 70.74 | 238 | 0 | 0 1.4.22 | | 49.03 | 52.23 | 227 | 2.47 | 0.88 1.4.46 | | 49.03 | 46.68 | 227 | 2.4 | 0.69 1.4.38 | | 48.17 | 84.06 | 223 | 0 | 0 1.4.139 | | 48.17 | 68.42 | 223 | 4.02 | 1.74 1.4.140 | | 48.17 | 54.4 | 223 | 3 | 0.88 1.4.145 | | 45.79 | 70.16 | 212 | 1.8 | 0.68 1.4.44 | | 44.71 | 54.41 | 207 | 1.7 | 0.59 1.4.30 | | 42.77 | 50.41 | 198 | 1.9 | 0.67 1.4.72 | | 42.55 | 57.97 | 197 | 3.29 | 1.21 1.4.14 | | 42.34 | 66.92 | 196 | 0 | 0 1.4.23 | | 41.26 | 73.64 | 191 | 0 | 0 1.4.107 | | 40.61 | 54.09 | 188 | 3.65 | 1.13 1.4.138 | | 40.61 | 60.75 | 188 | 5.2 | 2.29 1.4.131 | | 39.31 | 51.21 | 182 | 3.65 | 1.41 1.4.29 | | 37.15 | 58.6 | 172 | 2.47 | 0.74 1.4.156 | | 36.07 | 47.27 | 167 | 2.47 | 0.94 1.4.53 | | 34.78 | 51.76 | 161 | 1.2 | 0.24 1.4.85 | | 34.34 | 45.34 | 159 | 3.23 | 1.38 1.4.159 | | 34.13 | 43.97 | 158 | 1.9 | 0.63 1.4.25 | | 33.48 | 43.28 | 155 | 1.34 | 0.4 1.4.65 | | 32.4 | 47.59 | 150 | 3 | 0.83 1.4.83 | | 32.4 | 54.44 | 150 | 0 | 0 1.4.13 | | 32.18 | 51.64 | 149 | 0 | 0 1.4.26 | | 32.18 | 44.02 | 149 | 1.2 | 0.29 1.4.90 | | 30.89 | 43.49 | 143 | 1.8 | 0.59 1.4.103 | | 30.89 | 47.51 | 143 | 1.7 | 0.5 1.4.37 | | 30.46 | 46.79 | 141 | 1.7 | 0.53 1.4.48 | | 30.02 | 59.94 | 139 | 3.7 | 1.41 1.4.68 | | 30.02 | 45.23 | 139 | 1.34 | 0.39 1.4.106 | | 29.81 | 50.49 | 138 | 3.84 | 1.92 1.4.11 | | 29.16 | 46.36 | 135 | 2.47 | 0.71 1.4.19 | | 29.16 | 41.75 | 135 | 1.7 | 0.34 1.4.89 | | 29.16 | 52.8 | 135 | 0 | 0 1.4.133 | | 29.16 | 43.63 | 135 | 1.34 | 0.43 1.4.49 | | 28.3 | 55.43 | 131 | 0 | 0 1.4.91 | | 28.3 | 46.14 | 131 | 0 | 0 1.4.36 | | 27.65 | 41.39 | 128 | 1.8 | 0.46 1.4.59 | | 27.43 | 53.74 | 127 | 0 | 0 1.4.5 | | 26.57 | 41.47 | 123 | 2.94 | 1.6 1.4.31 | | 26.57 | 36.9 | 123 | 1.34 | 0.34 1.4.21 | | 26.14 | 43.12 | 121 | 3.23 | 1.55 1.4.35 | | 26.14 | 46.24 | 121 | 0 | 0 1.4.111 | | 26.14 | 46.8 | 121 | 0 | 0 1.4.86 | | 25.27 | 43.38 | 117 | 0 | 0 1.4.120 | | 25.06 | 35.43 | 116 | 1.34 | 0.32 1.4.121 | | 24.62 | 38.5 | 114 | 2.62 | 1.45 1.4.143 | | 24.62 | 57.97 | 114 | 0 | 0 1.4.82 | | 24.19 | 33.83 | 112 | 2.08 | 0.75 1.4.158 | | 22.9 | 39.53 | 106 | 0.85 | 0.2 1.4.28 | | 22.68 | 35.36 | 105 | 2.24 | 0.88 1.4.75 | | 22.68 | 32.14 | 105 | 1.8 | 0.5 1.4.60 | | 22.25 | 36.32 | 103 | 1.2 | 0.24 1.4.4 | | 21.6 | 35.38 | 100 | 1.34 | 0.42 1.4.43 | | 20.74 | 41.19 | 96 | 0 | 0 1.4.141 | | 20.74 | 33.96 | 96 | 2.16 | 0.87 1.4.7 | | 20.52 | 36.4 | 95 | 0.85 | 0.19 1.4.16 | | 18.79 | 27.92 | 87 | 1.8 | 0.51 1.4.104 | | 18.79 | 20.06 | 87 | 0.85 | 0.23 1.4.137 | | 18.36 | 23.56 | 85 | 1.34 | 0.5 1.4.34 | | 17.5 | 25.82 | 81 | 1.8 | 0.5 1.4.41 | | 17.5 | 30.46 | 81 | 1.7 | 0.65 1.4.61 | | 17.28 | 25.41 | 80 | 1.2 | 0.32 1.4.80 | | 17.28 | 36.68 | 80 | 0 | 0 1.4.93 | | 17.28 | 36.68 | 80 | 0 | 0 1.4.97 | | 17.28 | 36.68 | 80 | 0 | 0 1.4.128 | | 17.28 | 21.6 | 80 | 0.85 | 0.26 1.4.2 | | 17.06 | 35.72 | 79 | 2.75 | 1.55 1.4.15 | | 16.85 | 32.3 | 78 | 0 | 0 1.4.39 | | 16.85 | 32.3 | 78 | 0 | 0 1.4.110 | | 14.69 | 21.77 | 68 | 1.2 | 0.3 1.4.152 | | 14.69 | 23 | 68 | 0.85 | 0.22 1.4.56 | | 14.26 | 25.14 | 66 | 1.99 | 0.85 1.4.70 | | 13.18 | 19.03 | 61 | 1.34 | 0.39 1.4.6 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.33 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.54 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.76 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.79 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.98 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.112 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.123 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.129 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.135 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.144 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.147 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.155 | | 12.31 | 29.54 | 57 | 0 | 0 1.4.109 | | 12.1 | 17.87 | 56 | 1.34 | 0.46 1.4.58 | | 11.66 | 22.28 | 54 | 1.47 | 0.59 1.4.148 | | 11.66 | 21.35 | 54 | 0.6 | 0.18 1.4.153 | | 11.45 | 20.68 | 53 | 1.34 | 0.52 1.4.92 | | 11.02 | 20.98 | 51 | 0.85 | 0.34 1.4.124 | | 10.58 | 19.41 | 49 | 0.85 | 0.21 1.4.71 | | 9.72 | 18 | 45 | 1.34 | 0.54 1.4.27 | | 9.29 | 15.54 | 43 | 0.6 | 0.11 1.4.47 | | 8.86 | 18.26 | 41 | 1.34 | 0.46 1.4.40 | | 8.42 | 19.26 | 39 | 1.2 | 0.48 1.4.142 | | 7.78 | 14.22 | 36 | 0.6 | 0.2 1.4.87 | | 7.34 | 13.01 | 34 | 1.2 | 0.32 1.4.146 | | 7.34 | 15.4 | 34 | 0.85 | 0.28 1.4.150 | | 7.34 | 17.59 | 34 | 1.2 | 0.41 1.4.10 | | 6.91 | 12.61 | 32 | 0.85 | 0.25 1.4.119 | | 6.91 | 13.51 | 32 | 0.85 | 0.18 1.4.74 | | 6.05 | 9.31 | 28 | 0.6 | 0.15 1.4.66 | | 5.83 | 12.01 | 27 | 0.85 | 0.33 1.4.1 | | 5.62 | 11.34 | 26 | 0.6 | 0.18 1.4.67 | | 5.62 | 11.34 | 26 | 0.6 | 0.18 1.4.55 | | 5.18 | 7.82 | 24 | 0.6 | 0.1 1.4.63 | | 5.18 | 11.37 | 24 | 0.85 | 0.24 1.4.101 | | 5.18 | 12.01 | 24 | 0.6 | 0.12 > close session > open ""/Users/nathansoper/Google Drive/My Drive/Lab - Tania/6th year > meetings/Figures/holo-RdRp.cxs"" format session > view name session-start opened ChimeraX session > select /P:33 20 atoms, 21 bonds, 1 residue, 1 model selected > select /P:35 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > ui tool show ViewDockX No suitable models found for ViewDockX > ui tool show ""Volume Viewer"" > toolshed show > ui tool show ""Find Cavities"" > surface #2.1 /T @ select /P:34 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /P:35 42 atoms, 45 bonds, 2 residues, 1 model selected > select add /P:33 62 atoms, 66 bonds, 3 residues, 1 model selected > select add /P:32 85 atoms, 91 bonds, 4 residues, 1 model selected > select add /P:31 107 atoms, 115 bonds, 5 residues, 1 model selected > select add /P:30 129 atoms, 139 bonds, 6 residues, 1 model selected > select add /P:29 152 atoms, 164 bonds, 7 residues, 1 model selected > select add /P:28 174 atoms, 188 bonds, 8 residues, 1 model selected > surface #2.1 /sel@ surface #2.1 sel @ Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGP3LL/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 13822.41.1 OS Loader Version: 13822.41.1 Software: System Software Overview: System Version: macOS 26.1 (25B78) Kernel Version: Darwin 25.1.0 Time since boot: 53 minutes, 16 seconds Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: P24q-30: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported DELL E2423H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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-MutationScores: 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 narwhals: 2.13.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 2.3.5 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 plotly: 6.5.0 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.8.4 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tomlkit: 0.13.3 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Graphics duplicate all ChimeraX