id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18056 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003217cf000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003207cc000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031f7c9000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031e7c6000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031d7c3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031c7c0000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031b7bd000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a7ba000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003197b7000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003187b4000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003177b1000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003167ae000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003157ab000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000202aa8200 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension 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, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, 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""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ { ""treatmentId"" : ""ccf01f2d-382e-4ccc-a332-b3f688bc9bbf"", ""experimentId"" : ""67f46b1a73932228c9baf274"", ""deploymentId"" : 400000001 } ] }, ""reportNotes"" : [ ""RIP register does not match crashing frame (0x0 vs 0x7FF89AE52AE0)"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 9blf Summary of feedback from opening 9blf fetched from pdb --- warnings | Atom H1 is not in the residue template for ALA /A:2 Atom H1 is not in the residue template for PHE /B:6 Atom H1 is not in the residue template for SER /C:1 Atom H1 is not in the residue template for PHE /D:6 note | Fetching compressed mmCIF 9blf from http://files.rcsb.org/download/9blf.cif 9blf title: SARS-CoV-2 core polymerase complex inhibited by araCTP [more info...] Chain information for 9blf #1 --- Chain | Description | UniProt A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 2-929 B D | Non-structural protein 8 | R1AB_SARS2 6-193 C | Non-structural protein 7 | R1A_SARS2 1-73 P | RNA (31-MER) | T | RNA (33-MER) | Non-standard residues in 9blf #1 --- CAR — cytosine arabinose-5'-phosphate HF4 — 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta- D-arabinofuranosyl}pyrimidin-2(1H)-one (Cytarabine-TRIPHOSPHATE) MG — magnesium ion ZN — zinc ion > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP > structure/Chimera/araUTP/SARS2 UTP-UTP_rebuild_04_rnk.pdb"" > ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP > structure/Chimera/araUTP/SARS2_araUTP_15_rnk.pdb"" > ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP > structure/Chimera/araUTP/SARS2 araUTP - UTP rebuild08_rnk.pdb"" Chain information for SARS2 UTP-UTP_rebuild_04_rnk.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available P | No description available T | No description available Chain information for SARS2_araUTP_15_rnk.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available P | No description available T | No description available Chain information for SARS2 araUTP - UTP rebuild08_rnk.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available P | No description available T | No description available > matchmaker #2-4 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 9blf, chain A (#1) with SARS2 UTP-UTP_rebuild_04_rnk.pdb, chain A (#2), sequence alignment score = 4682.2 RMSD between 927 pruned atom pairs is 0.364 angstroms; (across all 928 pairs: 0.379) Matchmaker 9blf, chain A (#1) with SARS2_araUTP_15_rnk.pdb, chain A (#3), sequence alignment score = 4681 RMSD between 925 pruned atom pairs is 0.373 angstroms; (across all 928 pairs: 0.393) Matchmaker 9blf, chain A (#1) with SARS2 araUTP - UTP rebuild08_rnk.pdb, chain A (#4), sequence alignment score = 4671.4 RMSD between 925 pruned atom pairs is 0.443 angstroms; (across all 928 pairs: 0.464) > show style stick Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > style stick Changed 60023 atom styles > delete H > view ligand > select ligand 87 atoms, 90 bonds, 3 residues, 2 models selected > select #1/A:1006@C2' 1 atom, 1 residue, 1 model selected > select up 29 atoms, 30 bonds, 1 residue, 1 model selected > view sel > color byhetero > set bgColor white > hide #!4 models > hide #!3 models > hide #!2 models > open 7uoe 7uoe title: SARS-CoV-2 replication-transcription complex bound to CTP, in a pre-catalytic state [more info...] Chain information for 7uoe #5 --- Chain | Description | UniProt A | RNA-directed RNA polymerase | R1AB_SARS2 1-932 B D | Non-structural protein 8 | R1AB_SARS2 1-198 C | Non-structural protein 7 | R1AB_SARS2 1-83 P | Product RNA (35-MER) | T | Template RNA (55-MER) | Non-standard residues in 7uoe #5 --- CTP — cytidine-5'-triphosphate L2B — 3'-deoxyuridine-5'-monophosphate ([(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl- oxolan-2-yl]methyl dihydrogen phosphate) MG — magnesium ion ZN — zinc ion > matchmaker #5 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 9blf, chain A (#1) with 7uoe, chain A (#5), sequence alignment score = 4731.4 RMSD between 917 pruned atom pairs is 0.957 angstroms; (across all 928 pairs: 1.004) > style stick Changed 61344 atom styles > color byhetero > open 6yyt 6yyt title: Structure of replicating SARS-CoV-2 polymerase [more info...] Chain information for 6yyt #6 --- Chain | Description | UniProt A | nsp12 | R1AB_SARS2 1-932 B D | nsp8 | R1AB_SARS2 1-198 C | nsp7 | R1AB_SARS2 1-83 P Q T U | RNA product | Non-standard residues in 6yyt #6 --- ZN — zinc ion > matchmaker #6 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 9blf, chain A (#1) with 6yyt, chain A (#6), sequence alignment score = 4617.4 RMSD between 840 pruned atom pairs is 0.695 angstroms; (across all 853 pairs: 0.848) > style stick Changed 72719 atom styles > color byhetero > hide #!5 models > hide #!6 models > show #!5 models > show #!2 models > hide #!5 models > hide #!1 models > hide #!2 models > show #!4 models > show #!5 models > show #!3 models > hide #!5 models > hide #!4 models > show #!1 models > show #!5 models > hide #!1 models > hide #!5 models > show #!6 models > show #!5 models > hide #!3 models > hide #!5 models > show #!2 models > hide #!6 models > show #!3 models > hide #!3 models > show #!6 models > close #6 > show #!5 models > hide #!5 models > show #!1 models > show #!3 models > hide #!3 models > hide #!2 models > hide #!1 models > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP > structure/Chimera/araUTP/SARS2_araUTP_15_rnk.pdb"" Chain information for SARS2_araUTP_15_rnk.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available D | No description available P | No description available T | No description available > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP > structure/Chimera/araUTP/SARS2 araUTP density map.mrc"" Opened SARS2 araUTP density map.mrc as #7, grid size 256,256,256, pixel 1.06, shown at level 0.151, step 1, values float32 > view #6 > volume #7 level 0.2634 > view ligand > style stick Changed 73464 atom styles > transparency 50 > select ligand 135 atoms, 140 bonds, 5 residues, 3 models selected > view #6 > volume #7 level 0.7138 > ui tool show ""Side View"" > select #6/P:30@O3' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > view sel > close #6-7 > info #1 3 models #1, 9blf, hidden 12293 atoms, 12678 bonds, 1444 residues, 6 chains (A,B,C,D,P,T) 63 hydrogen bonds, 12 metal coordination bonds #1.1, hydrogen bonds, shown, 63 pseudobonds #1.2, metal coordination bonds, shown, 12 pseudobonds > open 9blf Summary of feedback from opening 9blf fetched from pdb --- warnings | Atom H1 is not in the residue template for ALA /A:2 Atom H1 is not in the residue template for PHE /B:6 Atom H1 is not in the residue template for SER /C:1 Atom H1 is not in the residue template for PHE /D:6 9blf title: SARS-CoV-2 core polymerase complex inhibited by araCTP [more info...] Chain information for 9blf #6 --- Chain | Description | UniProt A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 2-929 B D | Non-structural protein 8 | R1AB_SARS2 6-193 C | Non-structural protein 7 | R1A_SARS2 1-73 P | RNA (31-MER) | T | RNA (33-MER) | Non-standard residues in 9blf #6 --- CAR — cytosine arabinose-5'-phosphate HF4 — 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta- D-arabinofuranosyl}pyrimidin-2(1H)-one (Cytarabine-TRIPHOSPHATE) MG — magnesium ion ZN — zinc ion > log metadata #6 Metadata for 9blf #6 --- Title | SARS-CoV-2 core polymerase complex inhibited by araCTP Citation | Anderson, T.K., Kirchdoerfer, R.N. (?). Structure of the SARS-CoV-2 core-RTC bound to RNA, araCMP, and araCTP. To Be Published Non-standard residues | CAR — cytosine arabinose-5'-phosphate HF4 — 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta- D-arabinofuranosyl}pyrimidin-2(1H)-one (Cytarabine-TRIPHOSPHATE) MG — magnesium ion ZN — zinc ion Gene sources | Severe acute respiratory syndrome coronavirus 2 synthetic construct CryoEM Map | EMDB 44654 — open map Experimental method | Electron microscopy Resolution | 3.31Å > open 44654 fromDatabase emdb Summary of feedback from opening 44654 fetched from emdb --- notes | Fetching compressed map 44654 from https://files.wwpdb.org/pub/emdb/structures/EMD-44654/map/emd_44654.map.gz Fetching map header 44654 from https://files.wwpdb.org/pub/emdb/structures/EMD-44654/header/emd-44654.xml Opened emdb 44654 as #7, grid size 256,256,256, pixel 1.06, shown at level 0.131, step 1, values float32, fit PDB 9blf > hide #!7 models > style stick Changed 85021 atom styles > delete H > color byhetero > select #6/P:31@C3' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > view sel > show #!7 models > volume #7 level 0.3668 > transparency 50 > show #!3 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > hide #!3 models > show #!5 models > hide #!5 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open 7uoe 7uoe title: SARS-CoV-2 replication-transcription complex bound to CTP, in a pre-catalytic state [more info...] Chain information for 7uoe #8 --- Chain | Description | UniProt A | RNA-directed RNA polymerase | R1AB_SARS2 1-932 B D | Non-structural protein 8 | R1AB_SARS2 1-198 C | Non-structural protein 7 | R1AB_SARS2 1-83 P | Product RNA (35-MER) | T | Template RNA (55-MER) | Non-standard residues in 7uoe #8 --- CTP — cytidine-5'-triphosphate L2B — 3'-deoxyuridine-5'-monophosphate ([(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl- oxolan-2-yl]methyl dihydrogen phosphate) MG — magnesium ion ZN — zinc ion > matchmaker #8 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 9blf, chain A (#1) with 7uoe, chain A (#8), sequence alignment score = 4731.4 RMSD between 917 pruned atom pairs is 0.957 angstroms; (across all 928 pairs: 1.004) > style stick Changed 86342 atom styles > color byhetero > close #8 > open 6yyt 6yyt title: Structure of replicating SARS-CoV-2 polymerase [more info...] Chain information for 6yyt #8 --- Chain | Description | UniProt A | nsp12 | R1AB_SARS2 1-932 B D | nsp8 | R1AB_SARS2 1-198 C | nsp7 | R1AB_SARS2 1-83 P Q T U | RNA product | Non-standard residues in 6yyt #8 --- ZN — zinc ion > matchmaker #8 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 9blf, chain A (#1) with 6yyt, chain A (#8), sequence alignment score = 4617.4 RMSD between 840 pruned atom pairs is 0.695 angstroms; (across all 853 pairs: 0.848) > style stick Changed 85012 atom styles > color byhetero > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!6 models > show #!3 models > show #!5 models > select #3/P:30@O3' 1 atom, 1 residue, 1 model selected > select add #8/P:18@O3' 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #3/P:30@O3' #8/P:18@O3' Distance between SARS2_araUTP_15_rnk.pdb #3/P UAT 30 O3' and 6yyt #8/P G 18 O3': 1.897Å > close #9 > hide #!7 models > hide #!5 models > hide #!3 models > hide #!8 models > show #!3 models > show #!8 models > hide #!3 models > open 7uo9 7uo9 title: SARS-CoV-2 replication-transcription complex bound to UTP, in a pre-catalytic state [more info...] Chain information for 7uo9 #9 --- Chain | Description | UniProt A | RNA-directed RNA polymerase | R1AB_SARS2 1-932 B D | Non-structural protein 8 | R1AB_SARS2 1-198 C | Non-structural protein 7 | R1AB_SARS2 1-83 P | Product RNA (35-MER) | T | Template RNA (55-MER) | Non-standard residues in 7uo9 #9 --- MG — magnesium ion UTP — uridine 5'-triphosphate ZN — zinc ion > matchmaker #9 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 9blf, chain A (#1) with 7uo9, chain A (#9), sequence alignment score = 4558.6 RMSD between 912 pruned atom pairs is 0.929 angstroms; (across all 926 pairs: 1.004) > style stick Changed 108875 atom styles > color byhetero > delete H > hide #!8 models > hide #!9 models > show #!1 models > show #!7 models > hide #!7 models > show #!2 models > hide #!1 models > hide #!2 models > show #!3 models > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP > structure/Chimera/araUTP/SARS2 araUTP density map.mrc"" Opened SARS2 araUTP density map.mrc as #10, grid size 256,256,256, pixel 1.06, shown at level 0.151, step 1, values float32 > open ""/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP > structure/Chimera/araUTP/SARS2_araUTP_15_rnk.pdb"" Chain information for SARS2_araUTP_15_rnk.pdb #11 --- Chain | Description A | No description available B | No description available C | No description available D | No description available P | No description available T | No description available > hide #!3 models > style stick Changed 109690 atom styles > delete H > transparency 50 > color byhetero > volume #10 level 0.8489 > select :H8 Nothing selected > select H Nothing selected > hide #!10 models > hide #!11 models > open 2lsc Summary of feedback from opening 2lsc fetched from pdb --- warnings | Atom HO5' is not in the residue template for CFL /A:1 Atom HO5' is not in the residue template for CFL /B:13 note | Fetching compressed mmCIF 2lsc from http://files.rcsb.org/download/2lsc.cif 2lsc title: Solution structure of 2'F-ANA and ANA self-complementary duplex [more info...] Chain information for 2lsc --- Chain | Description 12.1/A 12.2/A 12.3/A 12.4/A 12.5/A 12.6/A 12.7/A 12.8/A 12.9/A 12.10/A 12.11/A 12.12/A 12.13/A 12.14/A 12.15/A 12.16/A 12.17/A 12.18/A 12.19/A 12.20/A 12.1/B 12.2/B 12.3/B 12.4/B 12.5/B 12.6/B 12.7/B 12.8/B 12.9/B 12.10/B 12.11/B 12.12/B 12.13/B 12.14/B 12.15/B 12.16/B 12.17/B 12.18/B 12.19/B 12.20/B | DNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL)P*(A5O)P*(A5O)P*(UAR)P*(UAR)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3') > view #12 > delete #12.2-20 > ~ribbon #12 > select #12.1/A:6@O2' 1 atom, 1 residue, 1 model selected > select add #12.1/A:6@C8 2 atoms, 1 residue, 1 model selected > ui tool show Distances > distance #12.1/A:6@O2' #12.1/A:6@C8 Distance between 2lsc #12.1/A A5O 6 O2' and C8: 2.992Å > ~distance #12.1/A:6@O2' #12.1/A:6@C8 > select clear > select #12.1/A:6@C8 1 atom, 1 residue, 1 model selected > select add #12.1/A:5@O2' 2 atoms, 2 residues, 1 model selected > distance #12.1/A:6@C8 #12.1/A:5@O2' Distance between 2lsc #12.1/A A5O 6 C8 and A5O 5 O2': 3.285Å > addh H #12 Expected a keyword > addh #12 Summary of feedback from adding hydrogens to 2lsc #12.1 --- notes | Termini for 2lsc (#12.1) chain A determined from SEQRES records Termini for 2lsc (#12.1) chain B determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 42 hydrogen bonds 0 hydrogens added > ~distance #12.1/A:6@C8 #12.1/A:5@O2' > select add #12.1/A:5@C8 3 atoms, 2 residues, 1 model selected Exactly two atoms must be selected! > select clear > select #12.1/A:5@O2' 1 atom, 1 residue, 1 model selected > select add #12.1/A:5@C8 2 atoms, 1 residue, 1 model selected > distance #12.1/A:5@O2' #12.1/A:5@C8 Distance between 2lsc #12.1/A A5O 5 O2' and C8: 3.253Å > ~distance #12.1/A:5@O2' #12.1/A:5@C8 > select #12.1/A:5@HO2' 1 atom, 1 residue, 1 model selected > select clear > select #12.1/A:5@HO2' 1 atom, 1 residue, 1 model selected > select add #12.1/A:5@C8 2 atoms, 1 residue, 1 model selected > distance #12.1/A:5@HO2' #12.1/A:5@C8 Distance between 2lsc #12.1/A A5O 5 HO2' and C8: 3.024Å > select #12.1/B:21@C6 1 atom, 1 residue, 1 model selected > select add #12.1/B:21@F 2 atoms, 1 residue, 1 model selected > distance #12.1/B:21@C6 #12.1/B:21@F Distance between 2lsc #12.1/B CFL 21 C6 and F: 2.873Å > close #13 > hide #!12 models > show #!3 models > view #3 > select #3/P:30@C1' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > view sel ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Model Number: Z14Z00105LL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 25 days, 15 hours, 25 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: MZ279: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Main Display: Yes Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX