id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16989 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202405040553 (2024-05-04 05:53:31 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003b14af000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001eb4ffac0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 907 in atomspec_atoms File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 627 in _add_model_parts File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 476 in _check File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 490 in _check File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 490 in _check File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 470 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 612 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 455 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1011 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1008 in evaluate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1098 in evaluate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 36 in parse File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 71 in parse File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2776 in _parse_arg File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2922 in _process_positional_arguments File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3162 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py"", line 303 in run_matchmaker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 285 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1006 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1169 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, 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} ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8.dev202405040553 (2024-05-04) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6TNY fromDatabase pdb format mmcif Summary of feedback from opening 6TNY fetched from pdb --- note | Fetching compressed mmCIF 6tny from http://files.rcsb.org/download/6tny.cif 6tny title: Processive human polymerase δ holoenzyme [more info...] Chain information for 6tny #1 --- Chain | Description | UniProt A | DNA polymerase delta catalytic subunit | DPOD1_HUMAN 1-1107 B | DNA polymerase delta subunit 2 | DPOD2_HUMAN 1-469 C | DNA polymerase delta subunit 3 | DPOD3_HUMAN 2-466 D | DNA polymerase delta subunit 4 | DPOD4_HUMAN 2-107 E F G | Proliferating cell nuclear antigen | PCNA_HUMAN 1-261 P | DNA primer | T | DNA template | Non-standard residues in 6tny #1 --- DOC — 2',3'-dideoxycytidine-5'-monophosphate SF4 — iron/sulfur cluster TTP — thymidine-5'-triphosphate ZN — zinc ion 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > lighting soft > hide surfaces > hide cartoons > show cartoons > hide surfaces > select add #1 19722 atoms, 20206 bonds, 72 pseudobonds, 2452 residues, 4 models selected > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel cartoons > hide sel atoms > select subtract #1 9 models selected > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > select add #1 19722 atoms, 20206 bonds, 72 pseudobonds, 2452 residues, 4 models selected > hide sel atoms > show sel cartoons > select subtract #1 9 models selected > select /P 469 atoms, 525 bonds, 23 residues, 1 model selected > select nucleic-acid 1024 atoms, 1147 bonds, 55 pseudobonds, 50 residues, 2 models selected > show sel atoms > show sel cartoons > hide sel atoms > hide sel surfaces > show sel atoms > hide sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 1024 atom styles > nucleotides sel ladder > show sel cartoons > nucleotides sel ladder > nucleotides sel atoms > style nucleic & sel stick Changed 1024 atom styles > show sel atoms > select add #1 19722 atoms, 20206 bonds, 72 pseudobonds, 2452 residues, 6 models selected > select subtract #1 9 models selected > select /A 7960 atoms, 8132 bonds, 11 pseudobonds, 1013 residues, 3 models selected > color #1 #ba8571ff > undo > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > select add #1 19722 atoms, 20206 bonds, 72 pseudobonds, 2452 residues, 5 models selected > select subtract #1 9 models selected > select add #1 19722 atoms, 20206 bonds, 72 pseudobonds, 2452 residues, 4 models selected > hide sel cartoons > hide sel atoms > show sel cartoons > select subtract #1 9 models selected > select nucleic-acid 1024 atoms, 1147 bonds, 55 pseudobonds, 50 residues, 2 models selected > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 1024 atom styles > select add #1 19722 atoms, 20206 bonds, 72 pseudobonds, 2452 residues, 6 models selected > select subtract #1 9 models selected > select /A 7960 atoms, 8132 bonds, 11 pseudobonds, 1013 residues, 3 models selected > show #!1 target m > ui tool show ""Color Actions"" > color sel salmon > color sel dark salmon > color sel salmon > color sel green > color sel steel blue > color sel cadet blue > color sel slate blue > color sel medium slate blue > color sel coral > color sel tomato > color sel coral > select add #1 19722 atoms, 20206 bonds, 72 pseudobonds, 2452 residues, 5 models selected > select subtract #1 9 models selected > lighting soft > lighting full > lighting simple > lighting full > select ::name=""TTP"" 29 atoms, 30 bonds, 1 residue, 1 model selected > select add #1 19722 atoms, 20206 bonds, 72 pseudobonds, 2452 residues, 4 models selected > select subtract #1 9 models selected > select ::name=""TTP"" 29 atoms, 30 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > ui tool show H-Bonds > hbonds sel reveal true 9 hydrogen bonds found > hbonds sel reveal true 9 hydrogen bonds found > hide sel atoms > show sel atoms > select add #1 19722 atoms, 20206 bonds, 26 pseudobonds, 2452 residues, 4 models selected > select subtract #1 9 models selected > hide atoms > show atoms > undo > select ::name=""TTP"" 29 atoms, 30 bonds, 1 pseudobond, 1 residue, 2 models selected > hide sel atoms > show sel atoms > hide sel cartoons > show sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > hide sel atoms > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 29 atom styles > select add #1 19722 atoms, 20206 bonds, 26 pseudobonds, 2452 residues, 4 models selected > style sel stick Changed 19722 atom styles > select subtract #1 9 models selected > select ::name=""TTP"" 29 atoms, 30 bonds, 1 pseudobond, 1 residue, 2 models selected > color (#!1 & sel) hot pink > color (#!1 & sel) cyan > color (#!1 & sel) light sea green > color (#!1 & sel) byhetero > hide #1.3 models > hide #1.2 models > hide #1.1 models > show #1.1 models > ui tool show ""Show Sequence Viewer"" > ui tool show ""Side View"" > lighting soft > lighting simple > lighting full > lighting flat > lighting full > lighting soft > lighting full > lighting flat > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting shadows false > graphics silhouettes false > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:294-338 356 atoms, 367 bonds, 45 residues, 1 model selected > select /A:294-329 283 atoms, 293 bonds, 36 residues, 1 model selected > select /A:294-345 411 atoms, 424 bonds, 52 residues, 1 model selected > select > /A:160-169,173-177,216-228,249-259,301-306,373-389,401-413,459-467,473-482,493-499,501-540,544-548,551-564,605-614,617-619,655-675,679-705,713-739,767-783,837-853,856-873,898-906,941-949,953-960,962-971,976-990,1001-1005,1033-1063,1077-1096 3294 atoms, 3320 bonds, 407 residues, 1 model selected > select /A:294-345 411 atoms, 424 bonds, 52 residues, 1 model selected > select > /A:160-169,173-177,216-228,249-259,301-306,373-389,401-413,459-467,473-482,493-499,501-540,544-548,551-564,605-614,617-619,655-675,679-705,713-739,767-783,837-853,856-873,898-906,941-949,953-960,962-971,976-990,1001-1005,1033-1063,1077-1096 3294 atoms, 3320 bonds, 407 residues, 1 model selected > select /A:692 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:692-693 13 atoms, 12 bonds, 2 residues, 1 model selected > select > /A:94-105,123-131,136-142,147-151,192-195,207-213,265-268,286-291,296-298,311-319,334-343,351-356,367-370,392-395,431-438,442-449,455-458,592-594,598-603,621-622,637-639,645-647,750-754,758-762,792-805,808-814,824-827,883-886,921-926,939-940,992-993 1442 atoms, 1444 bonds, 176 residues, 1 model selected > select /A:693 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:693 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:694 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:694 9 atoms, 8 bonds, 1 residue, 1 model selected > select > /A:160-169,173-177,216-228,249-259,301-306,373-389,401-413,459-467,473-482,493-499,501-540,544-548,551-564,605-614,617-619,655-675,679-705,713-739,767-783,837-853,856-873,898-906,941-949,953-960,962-971,976-990,1001-1005,1033-1063,1077-1096 3294 atoms, 3320 bonds, 407 residues, 1 model selected > select /A:667 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:667 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:694 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:694 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:667 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:667 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:694 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:667 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:694 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!1 & sel) byhetero > select /A:667 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) byhetero > color (#!1 & sel) cornflower blue > color (#!1 & sel) byhetero > color (#!1 & sel) yellow > color (#!1 & sel) byhetero > select /A:694 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!1 & sel) yellow > color (#!1 & sel) byhetero > select > /A:160-169,173-177,216-228,249-259,301-306,373-389,401-413,459-467,473-482,493-499,501-540,544-548,551-564,605-614,617-619,655-675,679-705,713-739,767-783,837-853,856-873,898-906,941-949,953-960,962-971,976-990,1001-1005,1033-1063,1077-1096 3294 atoms, 3320 bonds, 407 residues, 1 model selected > select subtract #1.4 1 model selected > save /Users/kevinwang/Desktop/image1.png supersample 3 > close session > open 1rtd fromDatabase pdb format mmcif Summary of feedback from opening 1rtd fetched from pdb --- notes | Fetching compressed mmCIF 1rtd from http://files.rcsb.org/download/1rtd.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 1rtd title: Structure of A catalytic complex of hiv-1 reverse transcriptase: implications for nucleoside analog drug resistance [more info...] Chain information for 1rtd #1 --- Chain | Description | UniProt A C | PROTEIN (REVERSE TRANSCRIPTASE) | POL_HV1B1 1-554 B D | PROTEIN (REVERSE TRANSCRIPTASE) | POL_HV1H2 1-440 E G | DNA TEMPLATE FOR REVERSE TRANSCRIPTASE | F H | DNA PRIMER FOR REVERSE TRANSCRIPTASE | Non-standard residues in 1rtd #1 --- MG — magnesium ion TTP — thymidine-5'-triphosphate 1rtd mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > select add #1 17784 atoms, 18433 bonds, 141 pseudobonds, 2036 residues, 4 models selected > hide sel atoms > show sel cartoons > select subtract #1 Nothing selected > open 3v81 fromDatabase pdb format mmcif Summary of feedback from opening 3v81 fetched from pdb --- note | Fetching compressed mmCIF 3v81 from http://files.rcsb.org/download/3v81.cif 3v81 title: Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside inhibitor nevirapine [more info...] Chain information for 3v81 #2 --- Chain | Description | UniProt A C | HIV-1 Reverse Transcriptase P66 subunit | POL_HV1B1 1-554 B D | HIV-1 Reverse Transcriptase P51 subunit | POL_HV1B1 1-428 E T | DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') | F P | DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3') | Non-standard residues in 3v81 #2 --- ATM — 3'-azido-3'-deoxythymidine-5'-monophosphate MRG — N2-(3-mercaptopropyl)-2'-deoxyguanosine-5'-monophosphate NVP — 11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-B:2',3'-E][1,4]diazepin-6-one (non-nucleoside RT inhibitor nevirapine) 3v81 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select add #2 17510 atoms, 18144 bonds, 102 pseudobonds, 2016 residues, 3 models selected > hide sel atoms > show sel cartoons > select subtract #2 Nothing selected > ui tool show Matchmaker > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1rtd, chain A (#1) with 3v81, chain A (#2), sequence alignment score = 2756.8 RMSD between 311 pruned atom pairs is 0.794 angstroms; (across all 554 pairs: 3.284) > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #1.1 models > show #1.1 models > hide #1.2 models > show #1.2 models > sym #2 assembly 1 Made 1 copies for 3v81 assembly 1 > view > sym #2 assembly 2 Made 1 copies for 3v81 assembly 2 > view > sym #2 assembly 1 Made 1 copies for 3v81 assembly 1 > view > sym #2 assembly 1 Made 1 copies for 3v81 assembly 1 > view > sym #2 assembly 2 Made 1 copies for 3v81 assembly 2 > view > sym #2 assembly 1 Made 1 copies for 3v81 assembly 1 > view > sym #2 assembly 1 Made 1 copies for 3v81 assembly 1 > view > sym #2 assembly 1 Made 1 copies for 3v81 assembly 1 > view > sym #2 assembly 2 Made 1 copies for 3v81 assembly 2 > view > sym #2 assembly 2 Made 1 copies for 3v81 assembly 2 > view > sym #1 assembly 1 Made 1 copies for 1rtd assembly 1 > view > sym #1 assembly 2 Made 1 copies for 1rtd assembly 2 > view > select add #3 8755 atoms, 9072 bonds, 52 pseudobonds, 1008 residues, 4 models selected > hide #!3 models > show #!3 models > select subtract #3 Nothing selected > close session > open 1rtd format mmcif fromDatabase pdb 1rtd title: Structure of A catalytic complex of hiv-1 reverse transcriptase: implications for nucleoside analog drug resistance [more info...] Chain information for 1rtd #1 --- Chain | Description | UniProt A C | PROTEIN (REVERSE TRANSCRIPTASE) | POL_HV1B1 1-554 B D | PROTEIN (REVERSE TRANSCRIPTASE) | POL_HV1H2 1-440 E G | DNA TEMPLATE FOR REVERSE TRANSCRIPTASE | F H | DNA PRIMER FOR REVERSE TRANSCRIPTASE | Non-standard residues in 1rtd #1 --- MG — magnesium ion TTP — thymidine-5'-triphosphate 1rtd mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > sym #1 assembly 1 Made 1 copies for 1rtd assembly 1 > view > hide #1.1 models > hide #1.2 models > hide #1.3 models > hide #!2.1 atoms > show #!2.1 cartoons > select add #2.1.2 15 pseudobonds, 1 model selected > hide #2.1.2 models > show #2.1.2 models > select subtract #2.1.2 Nothing selected > select ::name=""TTP"" 87 atoms, 90 bonds, 3 residues, 2 models selected > show sel & #!2.1 atoms > ui tool show H-Bonds > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 1rtd #1/C PRO 468 N 42 hydrogen bonds found > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/C #2.1/A Alignment identifier is 1 > select > #1/A,C:60-64,71-75,105-110,179-183,186-191,227-229,232-234,239-241,326-331,337-342,348-354,388-391,414-416,438-446,453-459,464-469,492-497,530-535 > #2.1/A:60-64,71-75,105-110,179-183,186-191,227-229,232-234,239-241,326-331,337-342,348-354,388-391,414-416,438-446,453-459,464-469,492-497,530-535 2449 atoms, 2478 bonds, 288 residues, 2 models selected > select #1/A,C:64 #2.1/A:64 27 atoms, 24 bonds, 3 residues, 2 models selected > select #1/A,C:64 #2.1/A:64 27 atoms, 24 bonds, 3 residues, 2 models selected PROTEIN (REVERSE TRANSCRIPTASE) [ID: 1] region 3 chains [64] RMSD: 0.000 > select #1/A,C:65 #2.1/A:65 27 atoms, 24 bonds, 3 residues, 2 models selected > select #1/A,C:65 #2.1/A:65 27 atoms, 24 bonds, 3 residues, 2 models selected PROTEIN (REVERSE TRANSCRIPTASE) [ID: 1] region 3 chains [65] RMSD: 0.000 > show sel & #!2.1 atoms > nucleotides sel & #!2.1 atoms > style nucleic & sel & #!2.1 stick Changed 0 atom styles > nucleotides sel & #!2.1 atoms > style nucleic & sel & #!2.1 stick Changed 0 atom styles > hide sel & #!2.1 atoms > show sel & #!2.1 atoms > style sel & #!2.1 stick Changed 9 atom styles > color (#!2.1 & sel) cyan > color (#!2.1 & sel) byhetero > ui tool show ""Show Sequence Viewer"" > sequence chain #1/E #1/G #2.1/E Alignment identifier is 1 > select #1/E,G:3 #2.1/E:3 57 atoms, 63 bonds, 3 residues, 2 models selected > select #1/E,G:3-4 #2.1/E:3-4 114 atoms, 126 bonds, 6 residues, 2 models selected DNA TEMPLATE FOR REVERSE TRANSCRIPTASE [ID: 1] region 3 chains [3-4] RMSD: 0.000 > select #1/E,G:7 #2.1/E:7 57 atoms, 60 bonds, 3 residues, 2 models selected > select #1/E,G:7-20 #2.1/E:7-20 864 atoms, 969 bonds, 42 residues, 2 models selected DNA TEMPLATE FOR REVERSE TRANSCRIPTASE [ID: 1] region 3 chains [7-20] RMSD: 0.000 > select #1/E,G:6 #2.1/E:6 57 atoms, 60 bonds, 3 residues, 2 models selected > select #1/E,G:6 #2.1/E:6 57 atoms, 60 bonds, 3 residues, 2 models selected DNA TEMPLATE FOR REVERSE TRANSCRIPTASE [ID: 1] region 3 chains [6] RMSD: 0.000 > show sel & #!2.1 atoms > hide sel & #!2.1 atoms > select #1/E,G:4 #2.1/E:4 57 atoms, 60 bonds, 3 residues, 2 models selected > select #1/E,G:4 #2.1/E:4 57 atoms, 60 bonds, 3 residues, 2 models selected DNA TEMPLATE FOR REVERSE TRANSCRIPTASE [ID: 1] region 3 chains [4] RMSD: 0.000 > select #1/E,G:5-6 #2.1/E:5-6 120 atoms, 132 bonds, 6 residues, 2 models selected > select #1/E,G:5-6 #2.1/E:5-6 120 atoms, 132 bonds, 6 residues, 2 models selected DNA TEMPLATE FOR REVERSE TRANSCRIPTASE [ID: 1] region 3 chains [5-6] RMSD: 0.000 > select #1/E,G:5 #2.1/E:5 63 atoms, 69 bonds, 3 residues, 2 models selected > select #1/E,G:5 #2.1/E:5 63 atoms, 69 bonds, 3 residues, 2 models selected DNA TEMPLATE FOR REVERSE TRANSCRIPTASE [ID: 1] region 3 chains [5] RMSD: 0.000 > style sel & #!2.1 stick Changed 21 atom styles > color (#!2.1 & sel) byhetero > select ::name=""MG"" 10 atoms, 3 pseudobonds, 10 residues, 4 models selected > show sel & #!2.1 surfaces > ui tool show Contacts > ui tool show Distances No distances to delete! > ui tool show H-Bonds > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 1rtd #1/C PRO 468 N 0 hydrogen bonds found > select subtract #3 10 atoms, 3 pseudobonds, 10 residues, 5 models selected > select add #3 10 atoms, 3 pseudobonds, 10 residues, 5 models selected > close #3 > select ::name=""TTP"" 87 atoms, 90 bonds, 3 residues, 2 models selected > ui tool show H-Bonds > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 1rtd #1/C PRO 468 N 42 hydrogen bonds found > open 3v81 fromDatabase pdb format mmcif 3v81 title: Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside inhibitor nevirapine [more info...] Chain information for 3v81 #4 --- Chain | Description | UniProt A C | HIV-1 Reverse Transcriptase P66 subunit | POL_HV1B1 1-554 B D | HIV-1 Reverse Transcriptase P51 subunit | POL_HV1B1 1-428 E T | DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') | F P | DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3') | Non-standard residues in 3v81 #4 --- ATM — 3'-azido-3'-deoxythymidine-5'-monophosphate MRG — N2-(3-mercaptopropyl)-2'-deoxyguanosine-5'-monophosphate NVP — 11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-B:2',3'-E][1,4]diazepin-6-one (non-nucleoside RT inhibitor nevirapine) 3v81 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > sym #4 assembly 1 Made 1 copies for 3v81 assembly 1 > view > close #5 > show #!4 models > sym #4 assembly 1 Made 1 copies for 3v81 assembly 1 > view > close #4 > close #1 > select add #2.1 8894 atoms, 9218 bonds, 25 pseudobonds, 1019 residues, 4 models selected > select add #2 8894 atoms, 9218 bonds, 25 pseudobonds, 1019 residues, 6 models selected > select subtract #2 1 model selected > select add #5 8755 atoms, 9072 bonds, 52 pseudobonds, 1008 residues, 4 models selected > hide sel atoms > show sel cartoons > select subtract #5.1 1 model selected > select add #5 8755 atoms, 9072 bonds, 52 pseudobonds, 1008 residues, 4 models selected > select subtract #5 Nothing selected > ui tool show Matchmaker ===== Log before crash end ===== Log: You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8.dev202405040553 (2024-05-04) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,6 Model Number: Z176000KLLL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 96 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 17 days, 22 hours, 26 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.5 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.3 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.4 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202405040553 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 1.0.4 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.1 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core duplicate all ChimeraX