id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7670 Crash *probably* deleting MatchMaker chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000316096000 (most recent call first): File ""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File 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""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 2185 in _destroy File ""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 807 in remove_tool File ""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 370 in remove_tool File ""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py"", line 154 in delete File ""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop File ""/private/var/folders/dr/n_lp31fx58q_l53bm1fx0vkw0000gn/T/AppTranslocation/A45B2EBA-915C-4B69-81AE-9D3574A29FFB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 870 in init File 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0102.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0102.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -8.68376 Ignored bad PDB record found on line 9694 Irms 6.00161 Ignored bad PDB record found on line 9695 Irms_leg 5.42916 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0102.pdb #1 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0099.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0099.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -3.7403e-10 Ignored bad PDB record found on line 9694 Irms 30.9912 Ignored bad PDB record found on line 9695 Irms_leg 32.1051 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0099.pdb #2 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -3.15134 Ignored bad PDB record found on line 9694 Irms 7.20646 Ignored bad PDB record found on line 9695 Irms_leg 5.64961 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb #3 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0072.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0072.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -5.50336 Ignored bad PDB record found on line 9694 Irms 8.74348 Ignored bad PDB record found on line 9695 Irms_leg 7.85585 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0072.pdb #4 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0054.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0054.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 1 Ignored bad PDB record found on line 9692 Fnat 0.214286 Ignored bad PDB record found on line 9693 I_sc -2.75225 Ignored bad PDB record found on line 9694 Irms 2.53004 Ignored bad PDB record found on line 9695 Irms_leg 2.49518 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0054.pdb #5 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -6.41876e-10 Ignored bad PDB record found on line 9694 Irms 25.284 Ignored bad PDB record found on line 9695 Irms_leg 25.6332 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb #6 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > select #*/d,e 21648 atoms, 21876 bonds, 1386 residues, 6 models selected > show sel surfaces > select #*/L:24-42,57-69, 107-138 5172 atoms, 5220 bonds, 354 residues, 6 models selected > select #*/L 18378 atoms, 18612 bonds, 1206 residues, 6 models selected > color sel dark gray > select #*/L:24-42,57-69, 107-138 5172 atoms, 5220 bonds, 354 residues, 6 models selected > color sel light sea green > select #*/H 17994 atoms, 18222 bonds, 6 pseudobonds, 1224 residues, 12 models selected > color (#!1-6 & sel) light gray > select #*/H:24-42,57-69, 107-138 4914 atoms, 4986 bonds, 342 residues, 6 models selected > color sel cornflower blue > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > close #6 > show #!5 models > show #!4 models > show #!3 models > show #!2 models > show #!1 models > select #*/e:73-83 795 atoms, 795 bonds, 55 residues, 5 models selected > color (#!1-5 & sel) hot pink > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > show #!4 models > close #4 > show #!3 models > close #3 > show #!2 models > close #2 > show #!1 models > close #1 > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0540.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0540.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -3.39389 Ignored bad PDB record found on line 9694 Irms 10.4088 Ignored bad PDB record found on line 9695 Irms_leg 9.35688 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0540.pdb #1 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0527.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0527.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -7.57227 Ignored bad PDB record found on line 9694 Irms 9.69897 Ignored bad PDB record found on line 9695 Irms_leg 8.63842 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0527.pdb #2 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0919.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0919.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -4.9249 Ignored bad PDB record found on line 9694 Irms 5.70901 Ignored bad PDB record found on line 9695 Irms_leg 5.0121 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0919.pdb #3 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1868.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1868.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -1.66877 Ignored bad PDB record found on line 9694 Irms 8.06501 Ignored bad PDB record found on line 9695 Irms_leg 6.59623 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1868.pdb #4 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1315.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1315.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -3.91601 Ignored bad PDB record found on line 9694 Irms 8.62544 Ignored bad PDB record found on line 9695 Irms_leg 6.97779 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1315.pdb #6 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -3.15134 Ignored bad PDB record found on line 9694 Irms 7.20646 Ignored bad PDB record found on line 9695 Irms_leg 5.64961 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0091.pdb #7 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2054.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2054.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 1 Ignored bad PDB record found on line 9692 Fnat 0.142857 Ignored bad PDB record found on line 9693 I_sc -3.35916 Ignored bad PDB record found on line 9694 Irms 4.17874 Ignored bad PDB record found on line 9695 Irms_leg 3.50091 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2054.pdb #8 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0803.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0803.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -1.79567 Ignored bad PDB record found on line 9694 Irms 9.3712 Ignored bad PDB record found on line 9695 Irms_leg 8.43876 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0803.pdb #9 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0536.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0536.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0.0714286 Ignored bad PDB record found on line 9693 I_sc -7.42132 Ignored bad PDB record found on line 9694 Irms 5.30965 Ignored bad PDB record found on line 9695 Irms_leg 4.13428 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0536.pdb #10 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2402.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2402.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 1 Ignored bad PDB record found on line 9692 Fnat 0.214286 Ignored bad PDB record found on line 9693 I_sc -3.91057 Ignored bad PDB record found on line 9694 Irms 2.87454 Ignored bad PDB record found on line 9695 Irms_leg 2.49698 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2402.pdb #11 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1958.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1958.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -5.78107 Ignored bad PDB record found on line 9694 Irms 11.442 Ignored bad PDB record found on line 9695 Irms_leg 9.85159 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1958.pdb #12 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2795.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2795.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -0.000177861 Ignored bad PDB record found on line 9694 Irms 10.1235 Ignored bad PDB record found on line 9695 Irms_leg 9.88136 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2795.pdb #13 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -6.41876e-10 Ignored bad PDB record found on line 9694 Irms 25.284 Ignored bad PDB record found on line 9695 Irms_leg 25.6332 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0045.pdb #14 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0290.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0290.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -0.839759 Ignored bad PDB record found on line 9694 Irms 8.39478 Ignored bad PDB record found on line 9695 Irms_leg 7.69343 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0290.pdb #15 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0174.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0174.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -9.31914 Ignored bad PDB record found on line 9694 Irms 6.58641 Ignored bad PDB record found on line 9695 Irms_leg 6.15729 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0174.pdb #16 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1523.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1523.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -3.87471 Ignored bad PDB record found on line 9694 Irms 4.90735 Ignored bad PDB record found on line 9695 Irms_leg 4.55731 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1523.pdb #17 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2500.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2500.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 1 Ignored bad PDB record found on line 9692 Fnat 0.214286 Ignored bad PDB record found on line 9693 I_sc -5.25695 Ignored bad PDB record found on line 9694 Irms 3.36464 Ignored bad PDB record found on line 9695 Irms_leg 2.93762 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2500.pdb #18 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2541.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2541.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -2.77925 Ignored bad PDB record found on line 9694 Irms 7.79606 Ignored bad PDB record found on line 9695 Irms_leg 6.07049 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2541.pdb #19 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2949.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_2949.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0.0714286 Ignored bad PDB record found on line 9693 I_sc -2.79016 Ignored bad PDB record found on line 9694 Irms 5.82414 Ignored bad PDB record found on line 9695 Irms_leg 4.64252 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_2949.pdb #20 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1895.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_1895.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -4.94088 Ignored bad PDB record found on line 9694 Irms 9.19857 Ignored bad PDB record found on line 9695 Irms_leg 8.2817 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_1895.pdb #21 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0935.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0935.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -5.00562 Ignored bad PDB record found on line 9694 Irms 11.0117 Ignored bad PDB record found on line 9695 Irms_leg 10.1688 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0935.pdb #22 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > open > /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0219.pdb Summary of feedback from opening /Users/qiaofang/Desktop/H1_H2_docking/dir_no_clash/CD3de_3giz_L_oriH1H2_dummy_H3_0002_0219.pdb --- warnings | Ignored bad PDB record found on line 9691 CAPRI_rank 0 Ignored bad PDB record found on line 9692 Fnat 0 Ignored bad PDB record found on line 9693 I_sc -1.07733 Ignored bad PDB record found on line 9694 Irms 9.12215 Ignored bad PDB record found on line 9695 Irms_leg 7.35583 651 messages similar to the above omitted Chain information for CD3de_3giz_L_oriH1H2_dummy_H3_0002_0219.pdb #23 --- Chain | Description H | No description available L | No description available d | No description available e | No description available > select #*/H 68977 atoms, 69851 bonds, 23 pseudobonds, 4692 residues, 46 models selected > color (#!1-4,6-23 & sel) light gray > select #*/H:24-42,57-69, 107-138 18837 atoms, 19113 bonds, 1311 residues, 23 models selected > color (#!1-4,6-23 & sel) cornflower blue > select #*/L 70449 atoms, 71346 bonds, 4623 residues, 23 models selected > color (#!1-4,6-23 & sel) dark gray > select #*/d,e 82984 atoms, 83858 bonds, 5313 residues, 23 models selected > show sel & #!1-4,6-23 surfaces > select #*/e:73-83 3657 atoms, 3657 bonds, 253 residues, 23 models selected > color (#!1-4,6-23 & sel) hot pink > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!20 models > hide #!21 models > hide #!22 models > hide #!23 models > show #!1 models > close #1 > show #!2 models > close #2 > show #!3 models > close #3 > show #!4 models > close #4 > show #!5 models > close #5 > show #!6 models > close #6 > show #!7 models > close #7 > show #!8 models > hide #!8 models > show #!9 models > close #9 > show #!10 models > close #10 > show #!11 models > close #11 > show #!12 models > close #12 > show #!13 models > close #13 > show #!14 models > close #14 > show #!15 models > close #15 > show #!16 models > hide #!16 models > show #!17 models > show #!18 models > hide #!17 models > hide #!18 models > show #!19 models > close #19 > show #!20 models > close #20 > show #!21 models > close #21 > show #!22 models > close #22 > show #!23 models > close #23 > show #!8 models > show #!16 models > show #!17 models > show #!18 models > hide #!8 models > hide #!16 models > hide #!17 models > show #!17 models > hide #!18 models > show #!16 models > hide #!17 models > close #16 > show #!8 models > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/tyr.com_0001_16678.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/tyr.com_0001_16678.pdb --- warnings | Ignored bad PDB record found on line 3646 CAPRI_rank 2 Ignored bad PDB record found on line 3647 Fnat 0.5 Ignored bad PDB record found on line 3648 I_sc -6.552 Ignored bad PDB record found on line 3649 Irms 3.05 Ignored bad PDB record found on line 3650 Irms_leg 2.298 7 messages similar to the above omitted Chain information for tyr.com_0001_16678.pdb #1 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/tyr.com_0001_01731.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/tyr.com_0001_01731.pdb --- warnings | Ignored bad PDB record found on line 3646 CAPRI_rank 1 Ignored bad PDB record found on line 3647 Fnat 0.25 Ignored bad PDB record found on line 3648 I_sc -10.157 Ignored bad PDB record found on line 3649 Irms 4.479 Ignored bad PDB record found on line 3650 Irms_leg 2.184 7 messages similar to the above omitted Chain information for tyr.com_0001_01731.pdb #2 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_14925.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_14925.pdb --- warnings | Ignored bad PDB record found on line 3649 CAPRI_rank 1.84467e+19 Ignored bad PDB record found on line 3650 I_sc -9.313 Ignored bad PDB record found on line 3651 Irms 4.856 Ignored bad PDB record found on line 3652 cen_rms 16.873 Ignored bad PDB record found on line 3653 rms 19.691 5 messages similar to the above omitted Chain information for trp.com_0001_14925.pdb #3 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_10073.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_10073.pdb --- warnings | Ignored bad PDB record found on line 3649 CAPRI_rank 1.84467e+19 Ignored bad PDB record found on line 3650 I_sc -6.418 Ignored bad PDB record found on line 3651 Irms 4.645 Ignored bad PDB record found on line 3652 cen_rms 16.076 Ignored bad PDB record found on line 3653 rms 14.999 5 messages similar to the above omitted Chain information for trp.com_0001_10073.pdb #4 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_01950.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/trp.com_0001_01950.pdb --- warnings | Ignored bad PDB record found on line 3649 CAPRI_rank 1.84467e+19 Ignored bad PDB record found on line 3650 I_sc -6.506 Ignored bad PDB record found on line 3651 Irms 2.166 Ignored bad PDB record found on line 3652 cen_rms 16.366 Ignored bad PDB record found on line 3653 rms 6.561 5 messages similar to the above omitted Chain information for trp.com_0001_01950.pdb #5 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/thr.com_0001_13336.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/thr.com_0001_13336.pdb --- warnings | Ignored bad PDB record found on line 3639 CAPRI_rank 1 Ignored bad PDB record found on line 3640 Fnat 0.25 Ignored bad PDB record found on line 3641 I_sc -7.846 Ignored bad PDB record found on line 3642 Irms 2.789 Ignored bad PDB record found on line 3643 Irms_leg 2.637 7 messages similar to the above omitted Chain information for thr.com_0001_13336.pdb #6 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/thr.com_0001_11240.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/thr.com_0001_11240.pdb --- warnings | Ignored bad PDB record found on line 3639 CAPRI_rank 3 Ignored bad PDB record found on line 3640 Fnat 1 Ignored bad PDB record found on line 3641 I_sc -7.449 Ignored bad PDB record found on line 3642 Irms 0.812 Ignored bad PDB record found on line 3643 Irms_leg 0.734 7 messages similar to the above omitted Chain information for thr.com_0001_11240.pdb #7 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/phe.com_0001_18061.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/phe.com_0001_18061.pdb --- warnings | Ignored bad PDB record found on line 3645 CAPRI_rank 0 Ignored bad PDB record found on line 3646 Fnat 0 Ignored bad PDB record found on line 3647 I_sc -7.161 Ignored bad PDB record found on line 3648 Irms 7.124 Ignored bad PDB record found on line 3649 Irms_leg 5.407 7 messages similar to the above omitted Chain information for phe.com_0001_18061.pdb #9 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/phe.com_0001_01987.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/phe.com_0001_01987.pdb --- warnings | Ignored bad PDB record found on line 3645 CAPRI_rank 0 Ignored bad PDB record found on line 3646 Fnat 0 Ignored bad PDB record found on line 3647 I_sc -11.661 Ignored bad PDB record found on line 3648 Irms 3.555 Ignored bad PDB record found on line 3649 Irms_leg 2.975 7 messages similar to the above omitted Chain information for phe.com_0001_01987.pdb #10 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/lys.com_0001_09032.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/lys.com_0001_09032.pdb --- warnings | Ignored bad PDB record found on line 3647 CAPRI_rank 0 Ignored bad PDB record found on line 3648 Fnat 0.2 Ignored bad PDB record found on line 3649 I_sc -8.942 Ignored bad PDB record found on line 3650 Irms 3.773 Ignored bad PDB record found on line 3651 Irms_leg 4.029 7 messages similar to the above omitted Chain information for lys.com_0001_09032.pdb #11 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/lys.com_0001_06272.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/lys.com_0001_06272.pdb --- warnings | Ignored bad PDB record found on line 3647 CAPRI_rank 2 Ignored bad PDB record found on line 3648 Fnat 0.6 Ignored bad PDB record found on line 3649 I_sc -9.019 Ignored bad PDB record found on line 3650 Irms 2.253 Ignored bad PDB record found on line 3651 Irms_leg 1.996 7 messages similar to the above omitted Chain information for lys.com_0001_06272.pdb #12 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/asp.com_0001_04115.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/asp.com_0001_04115.pdb --- warnings | Ignored bad PDB record found on line 3637 CAPRI_rank 0 Ignored bad PDB record found on line 3638 Fnat 0 Ignored bad PDB record found on line 3639 I_sc -6.118 Ignored bad PDB record found on line 3640 Irms 6.421 Ignored bad PDB record found on line 3641 Irms_leg 7.418 7 messages similar to the above omitted Chain information for asp.com_0001_04115.pdb #13 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_13296.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_13296.pdb --- warnings | Ignored bad PDB record found on line 3649 CAPRI_rank 2 Ignored bad PDB record found on line 3650 Fnat 0.5 Ignored bad PDB record found on line 3651 I_sc -8.83 Ignored bad PDB record found on line 3652 Irms 2.89 Ignored bad PDB record found on line 3653 Irms_leg 3.157 7 messages similar to the above omitted Chain information for arg.com_0001_13296.pdb #14 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_13266.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_13266.pdb --- warnings | Ignored bad PDB record found on line 3649 CAPRI_rank 2 Ignored bad PDB record found on line 3650 Fnat 0.5 Ignored bad PDB record found on line 3651 I_sc -8.657 Ignored bad PDB record found on line 3652 Irms 2.394 Ignored bad PDB record found on line 3653 Irms_leg 1.696 7 messages similar to the above omitted Chain information for arg.com_0001_13266.pdb #15 --- Chain | Description d | No description available e | No description available > open /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_12389.pdb Summary of feedback from opening /Users/qiaofang/Desktop/CD3de_disem/CD3de_dis/arg.com_0001_12389.pdb --- warnings | Ignored bad PDB record found on line 3649 CAPRI_rank 1 Ignored bad PDB record found on line 3650 Fnat 0.25 Ignored bad PDB record found on line 3651 I_sc -10.654 Ignored bad PDB record found on line 3652 Irms 4.412 Ignored bad PDB record found on line 3653 Irms_leg 3.808 7 messages similar to the above omitted Chain information for arg.com_0001_12389.pdb #16 --- Chain | Description d | No description available e | No description available > hide #1 models > show #1 models > ui tool show Matchmaker > matchmaker #8/d to #1/d 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 tyr.com_0001_16678.pdb, chain d (#1) with CD3de_3giz_L_oriH1H2_dummy_H3_0002_2054.pdb, chain d (#8), sequence alignment score = 512 RMSD between 68 pruned atom pairs is 0.828 angstroms; (across all 108 pairs: 3.137) ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 8 MB Memory: 8 GB Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 6 days 21:08 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Structure Comparison can't reproduce all ChimeraX