id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17940 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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""SIRI_TTS_DEVICE_TRAINING"" : ""6736733a26c1270f5a9ef53d"" }, ""deploymentId"" : 240000045 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/ctsai/Documents/AlphaFold_CyaB/Prediction_Fernando/CyaB_2_PilG2_model_0.cif CyaB_2_PilG2_model_0.cif title: . [more info...] Chain information for CyaB_2_PilG2_model_0.cif #1 --- Chain | Description A B | . C D | . Color CyaB_2_PilG2_model_0.cif by residue attribute pLDDT_score Computing secondary structure > set bgColor white > set bgColor #ffffff00 > select /C:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select /D:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select /C:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select /A:1-463 3610 atoms, 3677 bonds, 463 residues, 1 model selected > select /B:1-463 3610 atoms, 3677 bonds, 463 residues, 1 model selected > open /Users/ctsai/Documents/AlphaFold_CyaB/H0N27-0934_PAO-CyaB- > copy-2/pred.model_idx_0.rank_1.cif pred.model_idx_0.rank_1.cif title: Chai-1 predicted structure [more info...] Chain information for pred.model_idx_0.rank_1.cif #2 --- Chain | Description A B | protein-0-1 Color pred.model_idx_0.rank_1.cif by residue attribute pLDDT_score Computing secondary structure > close #1 > select #2/A:1-489 4021 atoms, 4120 bonds, 489 residues, 1 model selected > select #2/B:1-489 4021 atoms, 4120 bonds, 489 residues, 1 model selected > close session > open /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2/pred.rank_0.cif pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #1 --- Chain | Description A B | Entity A Color pred.rank_0.cif by residue attribute pLDDT_score Computing secondary structure > color #1 #2ea9dfff > color #1 #7ab8bfff > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif --- warnings | Unable to fetch template for 'LIG3': will connect using distance criteria Unable to fetch template for 'LIG4': will connect using distance criteria Unable to fetch template for 'LIG5': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria 1 messages similar to the above omitted pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #2 --- Chain | Description A B | Entity A Non-standard residues in pred.rank_0.cif #2 --- LIG3 — (LIG3) LIG4 — (LIG4) LIG5 — (LIG5) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) Color pred.rank_0.cif by residue attribute pLDDT_score Computing secondary structure > color #2 #f28f6bff > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure 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 pred.rank_0.cif, chain A (#1) with pred.rank_0.cif, chain A (#2), sequence alignment score = 2362.3 RMSD between 426 pruned atom pairs is 1.015 angstroms; (across all 463 pairs: 1.421) > close #1 > close > open ""/Volumes/Gani_sv_WS/Optical_tweezer/20241104_wt/20241104-141211 Marker > 2.h5"" Summary of feedback from opening /Volumes/Gani_sv_WS/Optical_tweezer/20241104_wt/20241104-141211 Marker 2.h5 --- notes | /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/17/JSON``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Marker/2``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( Failed opening file /Volumes/Gani_sv_WS/Optical_tweezer/20241104_wt/20241104-141211 Marker 2.h5: HDF5 file /Volumes/Gani_sv_WS/Optical_tweezer/20241104_wt/20241104-141211 Marker 2.h5 contains no 3d arrays > open /Users/ctsai/Documents/Model_building/Phenix/Final_models/SS- > bond/final_SS_resampled_WT_solid_woG1_Q23.pdb Chain information for final_SS_resampled_WT_solid_woG1_Q23.pdb #1 --- Chain | Description A B C D E F G H I J K L M N O P Q R S T U V | No description available > show cartoons > hide surfaces > hide cartoons > show cartoons > hide cartoons > hide atoms > show cartoons > dssp Computing secondary structure > select /C 1042 atoms, 1057 bonds, 143 residues, 1 model selected > select ~sel 21882 atoms, 22197 bonds, 3003 residues, 1 model selected > surface hidePatches sel > hide sel target a > cartoon hide sel > select /C:E48 Nothing selected Alignment identifier is 1 > select /N,A-M,O-V:48 198 atoms, 176 bonds, 22 residues, 1 model selected > select /N,A-M,O-V:48 198 atoms, 176 bonds, 22 residues, 1 model selected > select /C:48 9 atoms, 8 bonds, 1 residue, 1 model selected > color #1 #d92b04ff > select /C:23 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:75 4 atoms, 3 bonds, 1 residue, 1 model selected > select /C:30 11 atoms, 10 bonds, 1 residue, 1 model selected > close > open ""/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-173350 > Marker 10.h5"" Failed opening file /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-173350 Marker 10.h5: HDF5 error back trace File ""H5F.c"", line 836, in H5Fopen unable to synchronously open file File ""H5F.c"", line 796, in H5F__open_api_common unable to open file File ""H5VLcallback.c"", line 3863, in H5VL_file_open open failed File ""H5VLcallback.c"", line 3675, in H5VL__file_open open failed File ""H5VLnative_file.c"", line 128, in H5VL__native_file_open unable to open file File ""H5Fint.c"", line 1910, in H5F_open unable to lock the file File ""H5FD.c"", line 2412, in H5FD_lock driver lock request failed File ""H5FDsec2.c"", line 941, in H5FD__sec2_lock unable to lock file, errno = 35, error message = 'Resource temporarily unavailable' End of HDF5 error back trace Unable to open/create file '/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-173350 Marker 10.h5' > open ""/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-181112 > Marker 14.h5"" Summary of feedback from opening /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-181112 Marker 14.h5 --- notes | /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/123/JSON``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Marker/14``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( Failed opening file /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-181112 Marker 14.h5: HDF5 file /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-181112 Marker 14.h5 contains no 3d arrays > open ""/Volumes/Gani_sv_WS/Optical_tweezer/20250303_wt/20250303-153026 Marker > 1.h5"" Summary of feedback from opening /Volumes/Gani_sv_WS/Optical_tweezer/20250303_wt/20250303-153026 Marker 1.h5 --- notes | /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/52/JSON``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/53/JSON``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Marker/1``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( Failed opening file /Volumes/Gani_sv_WS/Optical_tweezer/20250303_wt/20250303-153026 Marker 1.h5: HDF5 file /Volumes/Gani_sv_WS/Optical_tweezer/20250303_wt/20250303-153026 Marker 1.h5 contains no 3d arrays > open ""/Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-183158 > Marker 16.h5"" Summary of feedback from opening /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-183158 Marker 16.h5 --- notes | /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Calibration/141/JSON``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( /Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/group.py:1192: UserWarning: problems loading leaf ``/Marker/16``:: variable length strings are not supported yet The leaf will become an ``UnImplemented`` node. warnings.warn( Failed opening file /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-183158 Marker 16.h5: HDF5 file /Volumes/Gani_sv_WS/Optical_tweezer/20250331_R30E/20250331-183158 Marker 16.h5 contains no 3d arrays > open > /Users/ctsai/Documents/Fernando_binders/all_binders/1846_binder_AF_16_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb > format pdb Chain information for 1846_binder_AF_16_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #1 --- Chain | Description A | No description available B | No description available Computing secondary structure > close session > open /Users/ctsai/Documents/Model_building/mm_PilTs_I_9ewx_N.cxs format > session > set bgColor transparent opened ChimeraX session > set bgColor white > set bgColor #ffffff00 > hide #2 models > select #1:30 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1:75 4 atoms, 3 bonds, 1 residue, 1 model selected > color #1 #d92b04ff > select #1:23 9 atoms, 8 bonds, 1 residue, 1 model selected > close session > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif --- warnings | Unable to fetch template for 'LIG3': will connect using distance criteria Unable to fetch template for 'LIG4': will connect using distance criteria Unable to fetch template for 'LIG5': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria 1 messages similar to the above omitted pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #1 --- Chain | Description A B | Entity A Non-standard residues in pred.rank_0.cif #1 --- LIG3 — (LIG3) LIG4 — (LIG4) LIG5 — (LIG5) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) Color pred.rank_0.cif by residue attribute pLDDT_score Computing secondary structure > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/pred.rank_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/pred.rank_0.cif --- warnings | Unable to fetch template for 'LIG10': will connect using distance criteria Unable to fetch template for 'LIG5': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria Unable to fetch template for 'LIG8': will connect using distance criteria 1 messages similar to the above omitted pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #2 --- Chain | Description A B | Entity A C D | Entity C Non-standard residues in pred.rank_0.cif #2 --- LIG10 — (LIG10) LIG5 — (LIG5) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) LIG9 — (LIG9) Color pred.rank_0.cif by residue attribute pLDDT_score Computing secondary structure > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #2 models > close #1 > show #2 models > select ::name=""LIG10"" 1 atom, 1 residue, 1 model selected > select :LIG10 1 atom, 1 residue, 1 model selected > hide sel target a > select :LIG5 31 atoms, 33 bonds, 1 residue, 1 model selected > hide sel target a > select :LIG6 31 atoms, 33 bonds, 1 residue, 1 model selected > hide sel target a > select :LIG7 1 atom, 1 residue, 1 model selected > hide sel target a > select :LIG8 1 atom, 1 residue, 1 model selected > hide sel target a > select :LIG9 1 atom, 1 residue, 1 model selected > hide sel target a > show sel surfaces > hide sel cartoons > hide sel atoms > show sel surfaces > select :LIG9 1 atom, 1 residue, 1 model selected > select :LIG9 1 atom, 1 residue, 1 model selected > hide (#!2 & sel) target a > hide sel atoms > hide sel cartoons > show sel surfaces > select clear > show surfaces > hide cartoons > color #2 #986db2ff > select #2/C:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select #2/D:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select /C 1029 atoms, 1044 bonds, 135 residues, 1 model selected > color (#!2 & sel) #f28f6bff > select /D 1029 atoms, 1044 bonds, 135 residues, 1 model selected > color (#!2 & sel) #ebaaa9ff > color (#!2 & sel) #f28f6bff > graphics silhouettes true > lighting full > lighting shadows false > lighting flat > lighting shadows true intensity 0.5 > lighting soft > select clear > save > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/colored.cxs > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif --- warnings | Atom C_1 is not in the residue template for LIG /C:1 Atom C_1 is not in the residue template for LIG /D:1 pred.model_idx_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.model_idx_0.cif #1 --- Chain | Description A B | protein-0-1 E F | protein-2-1 Non-standard residues in pred.model_idx_0.cif #1 --- LIG — (LIG) Color pred.model_idx_0.cif by residue attribute pLDDT_score Computing secondary structure > hide #1 models > show #1 models > close #1 > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_0.cif --- warnings | Unable to fetch template for 'LIG4': will connect using distance criteria Unable to fetch template for 'LIG5': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria Unable to fetch template for 'LIG8': will connect using distance criteria 1 messages similar to the above omitted pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #1 --- Chain | Description A B | Entity A C | Entity C Non-standard residues in pred.rank_0.cif #1 --- LIG4 — (LIG4) LIG5 — (LIG5) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) LIG9 — (LIG9) Color pred.rank_0.cif by residue attribute pLDDT_score Computing secondary structure > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_0.cif --- warnings | Unable to fetch template for 'LIG4': will connect using distance criteria Unable to fetch template for 'LIG5': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria Unable to fetch template for 'LIG8': will connect using distance criteria 1 messages similar to the above omitted pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #3 --- Chain | Description A B | Entity A C | Entity C Non-standard residues in pred.rank_0.cif #3 --- LIG4 — (LIG4) LIG5 — (LIG5) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) LIG9 — (LIG9) Color pred.rank_0.cif by residue attribute pLDDT_score Computing secondary structure > close #3 > select #1/A,B #2/A,B 14440 atoms, 14708 bonds, 1852 residues, 2 models selected > ui tool show Matchmaker > matchmaker #!2 & sel to #1 & sel Computing secondary structure 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 pred.rank_0.cif, chain A (#1) with pred.rank_0.cif, chain A (#2), sequence alignment score = 2392.3 RMSD between 272 pruned atom pairs is 0.683 angstroms; (across all 463 pairs: 4.626) > select #1/A,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > select #1 11561 atoms, 11758 bonds, 1494 residues, 1 model selected > show sel surfaces > hide sel cartoons > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > select #1/C,D 4306 atoms, 4371 bonds, 563 residues, 1 model selected > select #1/C 4275 atoms, 4338 bonds, 562 residues, 1 model selected > color (#!1 & sel) #bdc0baff > color (#!1 & sel) #2ea9dfff > select #1/a,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > color (#!1 & sel) #986db2ff > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > select clear > show #!1 cartoons > hide #!1 surfaces > show #!1 surfaces > hide #!1 surfaces > show #!1 surfaces > hide #!1 surfaces > show #!1 surfaces > hide #!1 surfaces > show #!2 models > hide #!2 models > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-fimL-1-ATP-2-Mg-4/pred.rank_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-fimL-1-ATP-2-Mg-4/pred.rank_0.cif --- warnings | Unable to fetch template for 'LIG10': will connect using distance criteria Unable to fetch template for 'LIG11': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria Unable to fetch template for 'LIG8': will connect using distance criteria 1 messages similar to the above omitted pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #3 --- Chain | Description A B | Entity A C D | Entity C E | Entity E Non-standard residues in pred.rank_0.cif #3 --- LIG10 — (LIG10) LIG11 — (LIG11) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) LIG9 — (LIG9) Color pred.rank_0.cif by residue attribute pLDDT_score > show #3#!1 surfaces > hide #!1,3 surfaces > hide #!1,3 cartoons > hide #!1,3 atoms > show #!1,3 surfaces > select #2/A,B #3/A,B 14440 atoms, 14708 bonds, 1852 residues, 2 models selected > ui tool show Matchmaker > matchmaker #!3 & sel to #2 & sel Computing secondary structure 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 pred.rank_0.cif, chain A (#2) with pred.rank_0.cif, chain B (#3), sequence alignment score = 2381.5 RMSD between 397 pruned atom pairs is 0.718 angstroms; (across all 463 pairs: 3.708) > color #1 #bdc0baff > color #2 #986db2ff > color #2 #448f91ff > color #3 #448f91ff > color #1 #bdc0baff > color #2 #986db2ff > color #3 #7ba23fff > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!1 models > select #2/C,D 2058 atoms, 2088 bonds, 270 residues, 1 model selected > select #3/C,D 2058 atoms, 2088 bonds, 270 residues, 1 model selected > color (#!3 & sel) #eb7a77ff > select clear > show #!3 cartoons > hide #!3 surfaces > show #!2 models > hide #!3 models > hide #!2 cartoons > show #!2 cartoons > hide #!2 surfaces > show #!2 surfaces > show #!1 models > hide #!2 models > color #1 #986db2ff > select #2/C 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select #1/C 4275 atoms, 4338 bonds, 562 residues, 1 model selected > color (#!1 & sel) #2ea9dfff > select clear > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif --- warnings | Atom C_1 is not in the residue template for LIG /C:1 Atom C_1 is not in the residue template for LIG /D:1 pred.model_idx_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.model_idx_0.cif #4 --- Chain | Description A B | protein-0-1 E F | protein-2-1 Non-standard residues in pred.model_idx_0.cif #4 --- LIG — (LIG) Color pred.model_idx_0.cif by residue attribute pLDDT_score Computing secondary structure > hide #!1 models > close #4 > hide #2.1 models > show #2.1 models > select add #2.1 1 atom, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > hide sel surfaces > hide #!2 models > show #!2 models > select subtract #2.1 1 model selected > show #!2 cartoons > hide #!2 surfaces > select add #2.1 1 atom, 1 residue, 1 model selected > select subtract #2.1 1 model selected > select add #2.2 3610 atoms, 463 residues, 1 model selected > select subtract #2.2 1 model selected > select add #2.1 1 atom, 1 residue, 1 model selected > select subtract #2.1 1 model selected > select add #2.4 1029 atoms, 135 residues, 1 model selected > select subtract #2.4 1 model selected > select add #2.5 1029 atoms, 135 residues, 1 model selected > select subtract #2.5 1 model selected > close #3 > show #!1 models > hide #!2 models > select add #1.3 4275 atoms, 562 residues, 1 model selected > select subtract #1.3 1 model selected > select add #1.2 3610 atoms, 463 residues, 1 model selected > select subtract #1.2 1 model selected > select add #1.1 3610 atoms, 463 residues, 1 model selected > select subtract #1.1 1 model selected > select add #1.3 4275 atoms, 562 residues, 1 model selected > select subtract #1.3 1 model selected > hide #!1 cartoons > show #!1 cartoons > hide #!1 surfaces > close #1 > show #!2 models > hide #!2 models > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_1.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-fimL-2-ATP-2-Mg-4/pred.rank_1.cif --- warnings | Unable to fetch template for 'LIG4': will connect using distance criteria Unable to fetch template for 'LIG5': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria Unable to fetch template for 'LIG8': will connect using distance criteria 1 messages similar to the above omitted pred.rank_1.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_1.cif #1 --- Chain | Description A B | Entity A C | Entity C Non-standard residues in pred.rank_1.cif #1 --- LIG4 — (LIG4) LIG5 — (LIG5) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) LIG9 — (LIG9) Color pred.rank_1.cif by residue attribute pLDDT_score Computing secondary structure > color #1 #2ea9dfff > color #1 #bdc0baff > color #1 #986db2ff > color #1 #bdc0baff > ui tool show Matchmaker > matchmaker #1 to #2 Computing secondary structure 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 pred.rank_0.cif, chain A (#2) with pred.rank_1.cif, chain B (#1), sequence alignment score = 2377.9 RMSD between 335 pruned atom pairs is 0.991 angstroms; (across all 463 pairs: 3.127) > show #!2 models > select #1/A,B #2/A,B 14440 atoms, 14708 bonds, 1852 residues, 2 models selected > ui tool show Matchmaker > matchmaker #1 & sel to #2 & sel Computing secondary structure 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 pred.rank_0.cif, chain A (#2) with pred.rank_1.cif, chain B (#1), sequence alignment score = 2377.9 RMSD between 335 pruned atom pairs is 0.991 angstroms; (across all 463 pairs: 3.127) > select clear > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #!2 models > hide #1 models > show #!2 models > show #1 models > hide #!2 models > hide #1 models > show #!2 models > show #!2 surfaces > select #12/C,D Nothing selected > select #2/C,D 2058 atoms, 2088 bonds, 270 residues, 1 model selected > color (#!2 & sel) #f28f6bff > select clear > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/pred.rank_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/pred.rank_0.cif --- warnings | Unable to fetch template for 'LIG10': will connect using distance criteria Unable to fetch template for 'LIG5': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria Unable to fetch template for 'LIG8': will connect using distance criteria 1 messages similar to the above omitted pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #3 --- Chain | Description A B | Entity A C D | Entity C Non-standard residues in pred.rank_0.cif #3 --- LIG10 — (LIG10) LIG5 — (LIG5) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) LIG9 — (LIG9) Color pred.rank_0.cif by residue attribute pLDDT_score Computing secondary structure > hide #!2 models > close #3 > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif --- warnings | Atom C_1 is not in the residue template for LIG /C:1 Atom C_1 is not in the residue template for LIG /D:1 pred.model_idx_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.model_idx_0.cif #3 --- Chain | Description A B | protein-0-1 E F | protein-2-1 Non-standard residues in pred.model_idx_0.cif #3 --- LIG — (LIG) Color pred.model_idx_0.cif by residue attribute pLDDT_score Computing secondary structure > select :LIG 66 atoms, 66 bonds, 6 residues, 1 model selected > select #3/E:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select #3/F:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select #3/B:1-463 3610 atoms, 3677 bonds, 463 residues, 1 model selected > select #3/A:1-463 3610 atoms, 3677 bonds, 463 residues, 1 model selected > select #3/E:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select #3/F:1-135 1029 atoms, 1044 bonds, 135 residues, 1 model selected > select :LIG 66 atoms, 66 bonds, 6 residues, 1 model selected > close #3 > show #1 models > show #!2 models > hide #1 models > open > /Users/ctsai/Documents/AlphaFold_CyaB/Prediction_Fernando/CyaB_2_PilG2_model_0.cif CyaB_2_PilG2_model_0.cif title: . [more info...] Chain information for CyaB_2_PilG2_model_0.cif #3 --- Chain | Description A B | . C D | . Color CyaB_2_PilG2_model_0.cif by residue attribute pLDDT_score Computing secondary structure > color #3 #7ab8bfff > select #3/A,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > ui tool show Matchmaker > matchmaker #3 & sel to #2 & sel No 'to' model specified > matchmaker #3 & sel to #2 Computing secondary structure 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 pred.rank_0.cif, chain A (#2) with CyaB_2_PilG2_model_0.cif, chain A (#3), sequence alignment score = 2361.7 RMSD between 281 pruned atom pairs is 1.236 angstroms; (across all 463 pairs: 4.894) > show sel surfaces > select clear > close #1 > select #3/A,B #2/A,B 14440 atoms, 14708 bonds, 1852 residues, 2 models selected > show sel surfaces > color (#!2-3 & sel) #ffffffff > color (#!2-3 & sel) #ebebebff > color (#!2-3 & sel) #d6d6d6ff > select #3/C,D 2058 atoms, 2088 bonds, 270 residues, 1 model selected > color sel #7ba23fff > color sel #bec23fff > color sel #ddd23bff > surface hidePatches sel > select #2/C,D 2058 atoms, 2088 bonds, 270 residues, 1 model selected > surface hidePatches (#!2 & sel) > select #3/C,D 2058 atoms, 2088 bonds, 270 residues, 1 model selected > color sel #2ea9dfff > select clear > select #3/A,B #2/A,B 14440 atoms, 14708 bonds, 1852 residues, 2 models selected > color (#!2-3 & sel) #ffffffff > color (#!2-3 & sel) #ebebebff > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting full > lighting soft > lighting simple > lighting soft > color (#!2-3 & sel) #ebebebff > color (#!2-3 & sel) #ebebebf9 > color (#!2-3 & sel) #ebebebf2 > color (#!2-3 & sel) #ebebebeb > color (#!2-3 & sel) #ebebebd7 > color (#!2-3 & sel) #ebebebca > color (#!2-3 & sel) #ebebebc7 > color (#!2-3 & sel) #ebebebbe > color (#!2-3 & sel) #ebebebbc > color (#!2-3 & sel) #ebebebbe > color (#!2-3 & sel) #ebebebc3 > color (#!2-3 & sel) #ebebebc9 > color (#!2-3 & sel) #ebebebcb > color (#!2-3 & sel) #ebebebd2 > color (#!2-3 & sel) #ebebebd8 > color (#!2-3 & sel) #ebebebde > color (#!2-3 & sel) #ebebebdf > color (#!2-3 & sel) #ebebebcc > color (#!2-3 & sel) #ebebebc9 > color (#!2-3 & sel) #ebebebbe > color (#!2-3 & sel) #c0c0c0ff > color (#!2-3 & sel) #c0c0c0f0 > select clear > select #3/A,B #2/A,B 14440 atoms, 14708 bonds, 1852 residues, 2 models selected > color (#!2-3 & sel) #c0c0c0ef > color (#!2-3 & sel) #c0c0c0ea > color (#!2-3 & sel) #c0c0c0e6 > color (#!2-3 & sel) #c0c0c0e2 > color (#!2-3 & sel) #c0c0c0e0 > color (#!2-3 & sel) #c0c0c0dc > color (#!2-3 & sel) #c0c0c0d9 > color (#!2-3 & sel) #c0c0c0d4 > color (#!2-3 & sel) #c0c0c0ce > color (#!2-3 & sel) #c0c0c0c4 > color (#!2-3 & sel) #c0c0c0b9 > color (#!2-3 & sel) #c0c0c0ae > color (#!2-3 & sel) #c0c0c0ab > color (#!2-3 & sel) #c0c0c0aa > color (#!2-3 & sel) #c0c0c0a6 > color (#!2-3 & sel) #c0c0c0a0 > color (#!2-3 & sel) #c0c0c09d > color (#!2-3 & sel) #c0c0c09a > color (#!2-3 & sel) #c0c0c097 > color (#!2-3 & sel) #c0c0c090 > color (#!2-3 & sel) #c0c0c08a > color (#!2-3 & sel) #c0c0c082 > color (#!2-3 & sel) #c0c0c07d > color (#!2-3 & sel) #c0c0c078 > color (#!2-3 & sel) #c0c0c06d > color (#!2-3 & sel) #c0c0c066 > color (#!2-3 & sel) #c0c0c060 > color (#!2-3 & sel) #c0c0c05d > color (#!2-3 & sel) #c0c0c055 > color (#!2-3 & sel) #c0c0c051 > color (#!2-3 & sel) #c0c0c04e > color (#!2-3 & sel) #c0c0c04b > color (#!2-3 & sel) #c0c0c049 > color (#!2-3 & sel) #c0c0c046 > color (#!2-3 & sel) #c0c0c042 > color (#!2-3 & sel) #c0c0c03f > color (#!2-3 & sel) #c0c0c03c > color (#!2-3 & sel) #c0c0c03a > color (#!2-3 & sel) #c0c0c032 > color (#!2-3 & sel) #c0c0c031 > color (#!2-3 & sel) #c0c0c027 > color (#!2-3 & sel) #c0c0c018 > color (#!2-3 & sel) #c0c0c014 > color (#!2-3 & sel) #c0c0c00e > color (#!2-3 & sel) #c0c0c00d > color (#!2-3 & sel) #c0c0c00b > color (#!2-3 & sel) #c0c0c009 > color (#!2-3 & sel) #c0c0c018 > color (#!2-3 & sel) #c0c0c03b > color (#!2-3 & sel) #c0c0c057 > color (#!2-3 & sel) #c0c0c061 > color (#!2-3 & sel) #c0c0c064 > color (#!2-3 & sel) #c0c0c067 > color (#!2-3 & sel) #c0c0c068 > color (#!2-3 & sel) #c0c0c060 > color (#!2-3 & sel) #c0c0c05a > color (#!2-3 & sel) #c0c0c056 > color (#!2-3 & sel) #c0c0c053 > color (#!2-3 & sel) #c0c0c052 > color (#!2-3 & sel) #c0c0c051 > color (#!2-3 & sel) #c0c0c04d > color (#!2-3 & sel) #c0c0c043 > select clear > open > /Users/ctsai/Documents/AlphaFold_CyaB/ACIAD1397-copy-2/pred.model_idx_0.rank_3.cif pred.model_idx_0.rank_3.cif title: Chai-1 predicted structure [more info...] Chain information for pred.model_idx_0.rank_3.cif #1 --- Chain | Description A B | protein-0-1 Color pred.model_idx_0.rank_3.cif by residue attribute pLDDT_score Computing secondary structure > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #1 models > show #1 models > close #1 > save > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/chai1_alphafold3.cxs > close session > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/colored.cxs opened ChimeraX session > lighting soft > save /Users/ctsai/Desktop/image16.png supersample 3 > hide surfaces > show cartoons > hide atoms > save /Users/ctsai/Desktop/image17.png supersample 3 > open /Users/ctsai/Desktop/image17.png Opened multi-channel map image17.png as #1, 3 channels, grid size 1344,850,1, pixel 1, shown at step 1, values uint8 > open /Users/ctsai/Desktop/image16.png Opened multi-channel map image16.png as #3, 3 channels, grid size 1344,850,1, pixel 1, shown at step 1, values uint8 > undo > close session > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/chai1_alphafold3.cxs opened ChimeraX session > close session > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/colored.cxs > format session opened ChimeraX session > hide surfaces > show cartoons > hide atoms > lighting flat > lighting soft > lighting simple > lighting flat > save /Users/ctsai/Desktop/image18.png supersample 3 > open /Volumes/Gani_sv_WS/colloborative_projects/Fernando/CyaB-PilG- > MD/Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif Summary of feedback from opening /Volumes/Gani_sv_WS/colloborative_projects/Fernando/CyaB-PilG- MD/Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif --- warnings | Atom C_1 is not in the residue template for LIG /I:1 Atom C_1 is not in the residue template for LIG /J:1 Atom C_1 is not in the residue template for LIG /K:1 Atom C_1 is not in the residue template for LIG /L:1 Atom C_1 is not in the residue template for LIG /M:1 9 messages similar to the above omitted Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif title: Chai-1 predicted structure [more info...] Chain information for Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif #1 --- Chain | Description A B | CyaB_PilG_membrane_protein_2 C D | CyaB_PilG_membrane_protein_4 Non-standard residues in Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif #1 --- LIG — (LIG) Color Chai1_CyaB2_PIlG2_ATP2_Mg4_POPE.cif by residue attribute pLDDT_score Computing secondary structure > close #1 > close session No visible models! > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/chai1_alphafold3.cxs > format session opened ChimeraX session > hide #!3 models > color #2 #986db2ff > select #1/C,D Nothing selected > select #2/C,D 2058 atoms, 2088 bonds, 270 residues, 1 model selected > color (#!2 & sel) #f28f6bff > select clear > select #2/C,D@58 Nothing selected > select #2/C,D 2058 atoms, 2088 bonds, 270 residues, 1 model selected Alignment identifier is 1 > select #2/C-D:58 16 atoms, 14 bonds, 2 residues, 1 model selected > select #2/C-D:58 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > select clear > color #2 white > color #2 #ebebebff > close session > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-ATP-2-Mg2-4/pred.rank_0.cif --- warnings | Unable to fetch template for 'LIG3': will connect using distance criteria Unable to fetch template for 'LIG4': will connect using distance criteria Unable to fetch template for 'LIG5': will connect using distance criteria Unable to fetch template for 'LIG6': will connect using distance criteria Unable to fetch template for 'LIG7': will connect using distance criteria 1 messages similar to the above omitted pred.rank_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.rank_0.cif #1 --- Chain | Description A B | Entity A Non-standard residues in pred.rank_0.cif #1 --- LIG3 — (LIG3) LIG4 — (LIG4) LIG5 — (LIG5) LIG6 — (LIG6) LIG7 — (LIG7) LIG8 — (LIG8) Color pred.rank_0.cif by residue attribute pLDDT_score Computing secondary structure > hide atoms > show surfaces > color #1 #ebebebff > select #1/A,B:1-17 252 atoms, 256 bonds, 34 residues, 1 model selected > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif Summary of feedback from opening /Users/ctsai/Documents/AlphaFold_CyaB/cyaB-2-ATP-2-pilG-2-Mg-4/pred.model_idx_0.cif --- warnings | Atom C_1 is not in the residue template for LIG /C:1 Atom C_1 is not in the residue template for LIG /D:1 pred.model_idx_0.cif title: Chai-1 predicted structure [more info...] Chain information for pred.model_idx_0.cif #2 --- Chain | Description A B | protein-0-1 E F | protein-2-1 Non-standard residues in pred.model_idx_0.cif #2 --- LIG — (LIG) Color pred.model_idx_0.cif by residue attribute pLDDT_score Computing secondary structure > color #2 #bdc0baff > color #2 #787d7bff > select #1/A,B #2/A,B 14440 atoms, 14708 bonds, 1852 residues, 2 models selected > ui tool show Matchmaker > matchmaker #2 & sel to #1 & sel Computing secondary structure 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 pred.rank_0.cif, chain A (#1) with pred.model_idx_0.cif, chain A (#2), sequence alignment score = 2360.5 RMSD between 383 pruned atom pairs is 0.857 angstroms; (across all 463 pairs: 4.441) > select #1/A,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > select #1/A,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > color #2 #4f4f48ff > color #2 #d6d6d6ff > color #2 silver > color #2 #919191ff > color #2 #797979ff > color #2 #ebebebff > color #2 #ebebeb53 > color #2 #ebebebff > select #1/A,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > color (#!1 & sel) #ebebebff > color (#!1 & sel) #ebebebfe > color (#!1 & sel) #ebebebaf > color (#!1 & sel) #ebebebae > color (#!1 & sel) #ebebebad > color (#!1 & sel) #ebebeba5 > color (#!1 & sel) #ebebeba1 > color (#!1 & sel) #ebebeba0 > color (#!1 & sel) #ebebeb9f > color (#!1 & sel) #ebebeb99 > color (#!1 & sel) #ebebeb95 > color (#!1 & sel) #ebebeb90 > color (#!1 & sel) #ebebeb8a > color (#!1 & sel) #ebebeb87 > color (#!1 & sel) #ebebeb86 > color (#!1 & sel) #ebebeb84 > color (#!1 & sel) #ebebeb82 > color (#!1 & sel) #ebebeb7d > color (#!1 & sel) #ebebeb7a > color (#!1 & sel) #ebebeb78 > color (#!1 & sel) #ebebeb74 > hide #2 models > show #2 models > hide #2 models > color (#!1 & sel) #ebebeb74 > color (#!1 & sel) #ebebeb6f > color (#!1 & sel) #ebebeb69 > color (#!1 & sel) #ebebeb67 > color (#!1 & sel) #ebebeb65 > color (#!1 & sel) #ebebeb64 > color (#!1 & sel) #ebebeb62 > color (#!1 & sel) #ebebeb60 > color (#!1 & sel) #ebebeb5f > color (#!1 & sel) #ebebeb5d > color (#!1 & sel) #ebebeb5c > color (#!1 & sel) #ebebeb5a > color (#!1 & sel) #ebebeb58 > color (#!1 & sel) #ebebeb51 > color (#!1 & sel) #ebebeb4a > color (#!1 & sel) #ebebeb47 > color (#!1 & sel) #ebebeb45 > color (#!1 & sel) #ebebeb43 > color (#!1 & sel) #ebebeb42 > color (#!1 & sel) #ebebeb41 > color (#!1 & sel) #ebebeb3e > color (#!1 & sel) #ebebeb3b > color (#!1 & sel) #ebebeb39 > color (#!1 & sel) #ebebeb3b > color (#!1 & sel) #ebebeb3d > color (#!1 & sel) #ebebeb3e > color (#!1 & sel) #ebebeb40 > color (#!1 & sel) #ebebeb45 > color (#!1 & sel) #ebebeb4b > color (#!1 & sel) #ebebeb4e > color (#!1 & sel) #ebebeb50 > color (#!1 & sel) #ebebeb51 > select #1/A,B:1-17 252 atoms, 256 bonds, 34 residues, 1 model selected > hide sel surfaces > show sel cartoons > color (#!1 & sel) #986db2ff > select #2/A,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > show #2 models > hide #!1 models > show sel surfaces > select #2/ Expected an objects specifier or a keyword > select #2 9344 atoms, 9508 bonds, 1202 residues, 1 model selected > show sel surfaces > select #2/A,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > color (#!2 & sel) #4f4f48ff > color (#!2 & sel) #787d7bff > color (#!2 & sel) #787d7bfe > color (#!2 & sel) #787d7bf9 > color (#!2 & sel) #787d7bf6 > color (#!2 & sel) #787d7bf4 > color (#!2 & sel) #787d7be8 > color (#!2 & sel) #787d7bdc > color (#!2 & sel) #787d7bd9 > color (#!2 & sel) #787d7bd3 > color (#!2 & sel) #787d7bcd > color (#!2 & sel) #787d7bc9 > color (#!2 & sel) #787d7bc2 > color (#!2 & sel) #787d7bb9 > color (#!2 & sel) #787d7bb5 > color (#!2 & sel) #787d7bb2 > color (#!2 & sel) #787d7bb0 > color (#!2 & sel) #787d7bad > color (#!2 & sel) #787d7ba5 > color (#!2 & sel) #787d7ba2 > color (#!2 & sel) #787d7b9f > color (#!2 & sel) #787d7b9c > color (#!2 & sel) #787d7b98 > color (#!2 & sel) #787d7b94 > color (#!2 & sel) #787d7b90 > color (#!2 & sel) #787d7b8c > color (#!2 & sel) #787d7b88 > color (#!2 & sel) #787d7b87 > color (#!2 & sel) #787d7b84 > color (#!2 & sel) #787d7b82 > color (#!2 & sel) #787d7b79 > color (#!2 & sel) #787d7b75 > color (#!2 & sel) #787d7b73 > color (#!2 & sel) #787d7b72 > color (#!2 & sel) #787d7b71 > color (#!2 & sel) #787d7b70 > color (#!2 & sel) #787d7b6c > color (#!2 & sel) #787d7b69 > color (#!2 & sel) #787d7b68 > color (#!2 & sel) #787d7b66 > color (#!2 & sel) #787d7b65 > color (#!2 & sel) #787d7b64 > color (#!2 & sel) #787d7b61 > color (#!2 & sel) #787d7b5d > color (#!2 & sel) #787d7b5c > color (#!2 & sel) #787d7b5b > color (#!2 & sel) #787d7b5a > color (#!2 & sel) #787d7b59 > show #!1 models > hide #!1 models > color (#!2 & sel) #4f4f48ff > color (#!2 & sel) #4f4f48f2 > color (#!2 & sel) #4f4f48e9 > color (#!2 & sel) #4f4f48e4 > color (#!2 & sel) #4f4f48e1 > color (#!2 & sel) #4f4f48de > color (#!2 & sel) #4f4f48db > color (#!2 & sel) #4f4f48d9 > color (#!2 & sel) #4f4f48d7 > color (#!2 & sel) #4f4f48d6 > color (#!2 & sel) #4f4f48d5 > color (#!2 & sel) #4f4f48d1 > color (#!2 & sel) #4f4f48d0 > color (#!2 & sel) #4f4f48ce > color (#!2 & sel) #4f4f48cc > color (#!2 & sel) #4f4f48cb > color (#!2 & sel) #4f4f48c9 > color (#!2 & sel) #4f4f48c8 > color (#!2 & sel) #4f4f48c7 > color (#!2 & sel) #4f4f48c5 > color (#!2 & sel) #4f4f48c4 > color (#!2 & sel) #4f4f48bf > color (#!2 & sel) #4f4f48ba > color (#!2 & sel) #4f4f48ad > color (#!2 & sel) #4f4f48aa > color (#!2 & sel) #4f4f48a9 > color (#!2 & sel) #4f4f48a5 > color (#!2 & sel) #4f4f48a3 > color (#!2 & sel) #4f4f4899 > color (#!2 & sel) #4f4f4893 > color (#!2 & sel) #4f4f4891 > color (#!2 & sel) #4f4f4890 > color (#!2 & sel) #4f4f488f > show #!1 models > hide #!1 models > color (#!2 & sel) #4f4f488e > color (#!2 & sel) #4f4f488a > color (#!2 & sel) #4f4f4888 > color (#!2 & sel) #4f4f487d > color (#!2 & sel) #4f4f4877 > color (#!2 & sel) #4f4f4875 > color (#!2 & sel) #4f4f4873 > color (#!2 & sel) #4f4f4871 > color (#!2 & sel) #4f4f486f > color (#!2 & sel) #4f4f486d > color (#!2 & sel) #4f4f486c > color (#!2 & sel) #4f4f486a > color (#!2 & sel) #4f4f4868 > color (#!2 & sel) #4f4f4866 > color (#!2 & sel) #4f4f4865 > color (#!2 & sel) #4f4f4862 > color (#!2 & sel) #4f4f485f > color (#!2 & sel) #4f4f485d > color (#!2 & sel) #4f4f485b > color (#!2 & sel) #4f4f4859 > color (#!2 & sel) #4f4f4858 > color (#!2 & sel) #4f4f4857 > color (#!2 & sel) #4f4f4855 > color (#!2 & sel) #4f4f4853 > color (#!2 & sel) #4f4f4851 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #2/C,D 62 atoms, 66 bonds, 2 residues, 1 model selected > select #2/C,D 62 atoms, 66 bonds, 2 residues, 1 model selected > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > select #2/C 31 atoms, 33 bonds, 1 residue, 1 model selected > select #2/C,D 62 atoms, 66 bonds, 2 residues, 1 model selected > select #2/E,F 2058 atoms, 2088 bonds, 270 residues, 1 model selected > color (#!2 & sel) #f28f6bff > color (#!2 & sel) #f28f6bf6 > color (#!2 & sel) #f28f6beb > color (#!2 & sel) #f28f6bdc > color (#!2 & sel) #f28f6bcd > color (#!2 & sel) #f28f6bbe > color (#!2 & sel) #f28f6bb0 > color (#!2 & sel) #f28f6ba5 > color (#!2 & sel) #f28f6b9f > color (#!2 & sel) #f28f6b98 > color (#!2 & sel) #f28f6b8f > color (#!2 & sel) #f28f6b85 > color (#!2 & sel) #f28f6b76 > color (#!2 & sel) #f28f6b6b > color (#!2 & sel) #f28f6b69 > color (#!2 & sel) #f28f6b67 > color (#!2 & sel) #f28f6b66 > color (#!2 & sel) #f28f6b64 > color (#!2 & sel) #f28f6b63 > color (#!2 & sel) #f28f6b61 > color (#!2 & sel) #f28f6b60 > color (#!2 & sel) #f28f6b5f > color (#!2 & sel) #f28f6b5e > color (#!2 & sel) #f28f6b5d > color (#!2 & sel) #f28f6b5b > color (#!2 & sel) #f28f6b5a > color (#!2 & sel) #f28f6b59 > color (#!2 & sel) #f28f6b57 > color (#!2 & sel) #f28f6b55 > color (#!2 & sel) #f28f6b52 > color (#!2 & sel) #f28f6b51 > select #2/A,B:1-17 252 atoms, 256 bonds, 34 residues, 1 model selected > color (#!2 & sel) #2ea9dfff > hide sel surfaces > show #!1 models > select clear > view > ui tool show ""Side View"" > save > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/cyaB-w- > wo-pilG-1-17.cxs > select #2/C,D 62 atoms, 66 bonds, 2 residues, 1 model selected > select #2/E,F 2058 atoms, 2088 bonds, 270 residues, 1 model selected Alignment identifier is 1 > select #2/E-F:91 16 atoms, 14 bonds, 2 residues, 1 model selected > select #2/E-F:91-108 278 atoms, 280 bonds, 36 residues, 1 model selected > surface hidePatches (#!2 & sel) > cartoon hide (#!2 & sel) > undo > show surfaces > hide surfaces > undo > close session > open > /Users/ctsai/Documents/AlphaFold_CyaB/cyaB_wt-2-pilG-2-ATP-2-Mg2-4/cyaB-w- > wo-pilG-1-17.cxs format session opened ChimeraX session > select #2/E,F 2058 atoms, 2088 bonds, 270 residues, 1 model selected Alignment identifier is 1 > select #2/E-F:61 16 atoms, 14 bonds, 2 residues, 1 model selected > select #2/E-F:61-76 252 atoms, 254 bonds, 32 residues, 1 model selected > select #2/E-F:78 10 atoms, 8 bonds, 2 residues, 1 model selected > select #2/E-F:78-84 104 atoms, 106 bonds, 14 residues, 1 model selected > select #2/E-F:93 16 atoms, 14 bonds, 2 residues, 1 model selected > select #2/E-F:93-112 322 atoms, 328 bonds, 40 residues, 1 model selected > select #2/E-F:74-75 34 atoms, 32 bonds, 4 residues, 1 model selected > select #2/E-F:74-111 580 atoms, 588 bonds, 76 residues, 1 model selected > hide (#!2 & sel) target a > surface hidePatches (#!2 & sel) > cartoon hide (#!2 & sel) > surface (#!2 & sel) > select #2/E,F 2058 atoms, 2088 bonds, 270 residues, 1 model selected > surface (#!2 & sel) > cartoon (#!2 & sel) > select clear > select #2/A,B 7220 atoms, 7354 bonds, 926 residues, 1 model selected > color (#!2 & sel) #ebebebff > color (#!2 & sel) #ebebebfd > color (#!2 & sel) #ebebebfb > color (#!2 & sel) #ebebebf7 > color (#!2 & sel) #ebebebe6 > color (#!2 & sel) #ebebebd2 > color (#!2 & sel) #ebebebc8 > color (#!2 & sel) #ebebebc6 > color (#!2 & sel) #ebebebc4 > color (#!2 & sel) #ebebebb2 > color (#!2 & sel) #ebebeb9f > color (#!2 & sel) #ebebeb7c > color (#!2 & sel) #ebebeb65 > color (#!2 & sel) #ebebeb5b > color (#!2 & sel) #ebebeb59 > color (#!2 & sel) #ebebeb58 > color (#!2 & sel) #ebebeb50 > color (#!2 & sel) #ebebeb4c > color (#!2 & sel) #ebebeb49 > color (#!2 & sel) #ebebeb46 > color (#!2 & sel) #ebebeb44 > color (#!2 & sel) #ebebeb41 > color (#!2 & sel) #ebebeb3a > color (#!2 & sel) #ebebeb37 > color (#!2 & sel) #ebebeb36 > color (#!2 & sel) #ebebeb33 > color (#!2 & sel) #ebebeb32 > color (#!2 & sel) #ebebeb30 > color (#!2 & sel) #ebebeb2e > color (#!2 & sel) #ebebeb30 > color (#!2 & sel) #ebebeb33 > color (#!2 & sel) #ebebeb35 > color (#!2 & sel) #ebebeb36 > color (#!2 & sel) #ebebeb37 > color (#!2 & sel) #ebebeb38 > color (#!2 & sel) #ebebeb39 > color (#!2 & sel) #ebebeb3b > color (#!2 & sel) #ebebeb3d > color (#!2 & sel) #ebebeb3f > color (#!2 & sel) #ebebeb40 > color (#!2 & sel) #ebebeb41 > color (#!2 & sel) #ebebeb43 > color (#!2 & sel) #ebebeb44 > color (#!2 & sel) #ebebeb45 > color (#!2 & sel) #ebebeb46 > color (#!2 & sel) #ebebeb47 > color (#!2 & sel) #ebebeb48 > color (#!2 & sel) #ebebeb49 > color (#!2 & sel) #ebebeb4a > color (#!2 & sel) #ebebeb4b > color (#!2 & sel) #ebebeb4d > color (#!2 & sel) #ebebeb4e > color (#!2 & sel) #ebebeb4f > color (#!2 & sel) #ebebeb51 > color (#!2 & sel) #ebebeb50 > select clear > select #2/A,B:1-17 252 atoms, 256 bonds, 34 residues, 1 model selected > color (#!2 & sel) #2ea9dfff > color (#!2 & sel) #006284ff > color (#!2 & sel) #2ea9dfff > select clear > ui tool show ""Side View"" > hide #!2 models > save /Users/ctsai/Desktop/image19.png supersample 3 > hide #!1 models > show #!2 models > save /Users/ctsai/Desktop/image20.png supersample 3 > show #!1 models > save /Users/ctsai/Desktop/image21.png supersample 3 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16S00188SM/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.61.3 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 41 days, 23 hours, 2 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 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 BenQ GC2870: 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 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 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: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX