id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17041 Mac multi-display crash chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.7.1-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. Fatal Python error: Segmentation fault Thread 0x0000000315e4b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000314e3f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000313e33000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000312e27000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000311e1b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000310e0f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030fe03000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030edf7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030ddeb000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030cddf000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030bdd3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000201978f40 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, 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""logWritingSignature"" : ""8f96caec155fd00926acdbcfcdfaff9bc28b3905"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""62745b8e85854550ad70b6e4"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""6539d7f333b9b7499c6f1b63"" }, ""deploymentId"" : 240000073 } ], ""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 8RUC fromDatabase pdb format mmcif Summary of feedback from opening 8RUC fetched from pdb --- notes | Fetching compressed mmCIF 8ruc from http://files.rcsb.org/download/8ruc.cif Fetching CCD CAP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/CAP/CAP.cif Fetching CCD KCX from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/KCX/KCX.cif 8ruc title: Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate [more info...] Chain information for 8ruc #1 --- Chain | Description | UniProt A C E G | RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE | RBL_SPIOL 1-475 I J K L | RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE | RBS1_SPIOL 1-123 Non-standard residues in 8ruc #1 --- CAP — 2-carboxyarabinitol-1,5-diphosphate MG — magnesium ion 8ruc mmCIF Assemblies --- 1| author_and_software_defined_assembly > select /A:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > select /C:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > select /E:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > select /G:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > select /I:1-123 1033 atoms, 1068 bonds, 123 residues, 1 model selected > select /J:1-123 1033 atoms, 1068 bonds, 123 residues, 1 model selected > select /K:1-123 1033 atoms, 1068 bonds, 123 residues, 1 model selected > select /L:1-123 1033 atoms, 1068 bonds, 123 residues, 1 model selected > select clear > close session > open 1RXO fromDatabase pdb format mmcif Summary of feedback from opening 1RXO fetched from pdb --- notes | Fetching compressed mmCIF 1rxo from http://files.rcsb.org/download/1rxo.cif Fetching CCD RUB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/RUB/RUB.cif 1rxo title: Activated spinach rubisco In complex with its substrate ribulose-1,5-bisphosphate and calcium [more info...] Chain information for 1rxo #1 --- Chain | Description | UniProt B E H L | RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE | RBL_SPIOL 1-475 C F I S | RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE | RBS1_SPIOL 1-123 Non-standard residues in 1rxo #1 --- CA — calcium ion RUB — ribulose-1,5-diphosphate 1rxo mmCIF Assemblies --- 1| author_and_software_defined_assembly > close session > open 8RUC format mmcif fromDatabase pdb 8ruc title: Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate [more info...] Chain information for 8ruc #1 --- Chain | Description | UniProt A C E G | RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE | RBL_SPIOL 1-475 I J K L | RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE | RBS1_SPIOL 1-123 Non-standard residues in 8ruc #1 --- CAP — 2-carboxyarabinitol-1,5-diphosphate MG — magnesium ion 8ruc mmCIF Assemblies --- 1| author_and_software_defined_assembly > select /A:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > select /C:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > select /E:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > select /G:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > ui tool show ""Color Actions"" > color sel plum > select /L:1-123 1033 atoms, 1068 bonds, 123 residues, 1 model selected > color sel light blue > select /I:1-123 1033 atoms, 1068 bonds, 123 residues, 1 model selected > color sel light sky blue > color sel light blue > color sel sky blue > color sel light steel blue > color sel dark sea green > select /J:1-123 1033 atoms, 1068 bonds, 123 residues, 1 model selected > color sel dark sea green > select /K:1-123 1033 atoms, 1068 bonds, 123 residues, 1 model selected > color sel dark sea green > color sel bychain > select clear > color bychain > color bypolymer > select /G:9-475 3657 atoms, 3747 bonds, 467 residues, 1 model selected > color sel lavender > color sel peach puff > color sel navajo white > color sel peach puff > color sel lavender > color sel steel blue > color sel cornflower blue > color sel light steel blue > color sel light sky blue > color sel sky blue > color sel cornflower blue > ui tool show ""Basic Actions"" > select /A 3993 atoms, 3767 bonds, 6 pseudobonds, 783 residues, 2 models selected > select /C 3976 atoms, 3767 bonds, 6 pseudobonds, 766 residues, 2 models selected > select /A 3993 atoms, 3767 bonds, 6 pseudobonds, 783 residues, 2 models selected > color sel light steel blue > select /E 3959 atoms, 3767 bonds, 6 pseudobonds, 749 residues, 2 models selected > color sel light steel blue > select /E 3959 atoms, 3767 bonds, 6 pseudobonds, 749 residues, 2 models selected > select /E 3959 atoms, 3767 bonds, 6 pseudobonds, 749 residues, 2 models selected > select /E 3959 atoms, 3767 bonds, 6 pseudobonds, 749 residues, 2 models selected > select /G 3987 atoms, 3767 bonds, 6 pseudobonds, 777 residues, 2 models selected > select /A 3993 atoms, 3767 bonds, 6 pseudobonds, 783 residues, 2 models selected > select /C 3976 atoms, 3767 bonds, 6 pseudobonds, 766 residues, 2 models selected > color sel light steel blue > select /I 1117 atoms, 1068 bonds, 207 residues, 1 model selected > select /J 1111 atoms, 1068 bonds, 201 residues, 1 model selected > select /K 1110 atoms, 1068 bonds, 200 residues, 1 model selected > select /L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > color sel dark sea green > color sel forest green > color sel green > color sel dark sea green > select /L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > select /L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > select /K 1110 atoms, 1068 bonds, 200 residues, 1 model selected > color sel light green > color sel dark sea green > select /K 1110 atoms, 1068 bonds, 200 residues, 1 model selected > select /K 1110 atoms, 1068 bonds, 200 residues, 1 model selected > select /L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > select /J 1111 atoms, 1068 bonds, 201 residues, 1 model selected > color sel light green > color sel dark sea green > select /I 1117 atoms, 1068 bonds, 207 residues, 1 model selected > color sel dark sea green > select /L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > color sel medium sea green > select clear > set bgColor white > lighting shadows false > graphics silhouettes true > lighting shadows true > lighting shadows false > lighting shadows true > lighting simple > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting full > lighting simple > lighting soft > lighting full > graphics silhouettes false > graphics silhouettes true > select /I 1117 atoms, 1068 bonds, 207 residues, 1 model selected > select /L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > color sel teal > color sel yellow green > color sel plum > color sel forest green > select clear > select /L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > color sel lime green > color sel lawn green > color sel dark cyan > color sel steel blue > color sel medium aquamarine > color sel sea green > select clear > save ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC complex.cxs"" > select clear > lighting full > lighting soft > lighting full > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > select ::name=""HOH"" 1520 atoms, 1520 residues, 1 model selected > hide sel atoms > save ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC complex.cxs"" > movie record > turn y 2 180 > wait 180 > movie encode /Users/jefflawton/Desktop/movie1.mp4 Movie saved to /Users/jefflawton/Desktop/movie1.mp4 > hide sel atoms > select clear > hide atoms > select ::name=""CAP"" 84 atoms, 80 bonds, 4 residues, 1 model selected > show sel atoms > select clear Drag select of 21 atoms, 20 bonds > select clear Drag select of 21 atoms, 20 bonds > hide sel atoms Drag select of 21 atoms, 20 bonds > hide sel atoms Drag select of 21 atoms, 20 bonds > hide sel atoms Drag select of 21 atoms, 20 bonds > view sel > style sel ball Changed 21 atom styles > color sel byelement > select clear Drag select of 21 atoms, 20 bonds > select sel : show sel atoms > ui mousemode right zoom > style sel stick Changed 180 atom styles > color (#!1 & sel) byelement > select /G :175 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :173 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :298 10 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :327 10 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :402 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :401 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :377 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :329 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel atoms > ui tool show ""Side View"" > select /G :379 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :381 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :335 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :294 10 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :380 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :405 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :404 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel atoms > select /G :403 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel atoms > select ::name=""HOH"" 1520 atoms, 1520 residues, 1 model selected > hide sel atoms > select /G:476@MG 1 atom, 1 residue, 1 model selected > style sel sphere Changed 1 atom style > select clear > select /G:477@O6 1 atom, 1 residue, 1 model selected > select add /G:477@C 2 atoms, 1 residue, 1 model selected > select add /G:477@O7 3 atoms, 1 residue, 1 model selected > select /G:177@NZ 1 atom, 1 residue, 1 model selected > select add /G:477@O6 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance /G:177@NZ /G:477@O6 Distance between /G LYS 177 NZ and CAP 477 O6: 2.735Å > distance style radius 0.01 > distance style radius 0.05 > select clear > select add /G:334@NZ 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select add /G:477@O7 2 atoms, 2 residues, 1 model selected > distance /G:334@NZ /G:477@O7 Distance between /G LYS 334 NZ and CAP 477 O7: 2.968Å > select add /G:477@O3P 3 atoms, 2 residues, 1 model selected > select clear > select add /G:477@O3P 1 atom, 1 residue, 1 model selected > select add /G:334@NZ 2 atoms, 2 residues, 1 model selected > distance /G:477@O3P /G:334@NZ Distance between /G CAP 477 O3P and LYS 334 NZ: 2.917Å > select clear > select /G:295@NH2 1 atom, 1 residue, 1 model selected > select add /G:477@O4P 2 atoms, 2 residues, 1 model selected > distance /G:295@NH2 /G:477@O4P Distance between /G ARG 295 NH2 and CAP 477 O4P: 3.026Å > hide #2.1 models > ~distance /G:477@O3P /G:334@NZ > ~distance /G:295@NH2 /G:477@O4P > select clear > select /G :295 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > save ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC active site.cxs"" > distance style radius 0.05 > save ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC active site.cxs"" > save /Users/jefflawton/Desktop/image1.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/jefflawton/Desktop/movie1.mp4 Movie saved to /Users/jefflawton/Desktop/movie1.mp4 > select /G:477@C3 1 atom, 1 residue, 1 model selected > cofr sel > movie record > turn y 2 180 > wait 180 > movie encode /Users/jefflawton/Desktop/movie2.mp4 Movie saved to /Users/jefflawton/Desktop/movie2.mp4 > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/jefflawton/Desktop/movie3.mp4 Movie saved to /Users/jefflawton/Desktop/movie3.mp4 > save ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC active site.cxs"" > close session > open /Users/jefflawton/Downloads/8ruc.pdb1 8ruc.pdb1 title: Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate [more info...] Chain information for 8ruc.pdb1 --- Chain | Description 1.1/A 1.1/C 1.1/E 1.1/G | No description available 1.2/A 1.2/C 1.2/E 1.2/G | No description available 1.1/I 1.2/I 1.1/J 1.2/J 1.1/K 1.2/K 1.1/L 1.2/L | No description available > select ::name=""HOH"" 3040 atoms, 3040 residues, 2 models selected > hide sel atoms > color sel bychain > color sel byhetero > color sel bychain > color sel bypolymer > color sel bychain > ui tool show ""Basic Actions"" > select #1.1/A 3993 atoms, 3767 bonds, 6 pseudobonds, 783 residues, 2 models selected > select #1.1/C 3976 atoms, 3767 bonds, 6 pseudobonds, 766 residues, 2 models selected > select #1.1/A 3993 atoms, 3767 bonds, 6 pseudobonds, 783 residues, 2 models selected > select #1.1/C 3976 atoms, 3767 bonds, 6 pseudobonds, 766 residues, 2 models selected > ui tool show ""Color Actions"" > color sel slate blue > color sel light slate gray > color sel cadet blue > color sel cornflower blue > color sel medium aquamarine > color sel dark cyan > color sel light sky blue > select #1.1/C 3976 atoms, 3767 bonds, 6 pseudobonds, 766 residues, 2 models selected > select #1.1/A 3993 atoms, 3767 bonds, 6 pseudobonds, 783 residues, 2 models selected > color sel sky blue > color sel light sky blue > select #1.1/E 3959 atoms, 3767 bonds, 6 pseudobonds, 749 residues, 2 models selected > color sel light sky blue > select #1.1/G 3987 atoms, 3767 bonds, 6 pseudobonds, 777 residues, 2 models selected > color sel light sky blue > select #1.2/A 3993 atoms, 3767 bonds, 783 residues, 1 model selected > color sel light steel blue > select #1.2/C 3976 atoms, 3767 bonds, 766 residues, 1 model selected > color sel light steel blue > select #1.2/E 3959 atoms, 3767 bonds, 749 residues, 1 model selected > color sel light steel blue > select #1.2/G 3987 atoms, 3767 bonds, 777 residues, 1 model selected > color sel light steel blue > select #1.1/C 3976 atoms, 3767 bonds, 6 pseudobonds, 766 residues, 2 models selected > select #1.1/I 1117 atoms, 1068 bonds, 207 residues, 1 model selected > color sel light pink > color sel plum > color sel lavender > color sel plum > color sel thistle > color sel plum > color sel pale violet red > color sel plum > color sel medium orchid > color sel plum > color sel light salmon > color sel pink > color sel plum > select #1.1/J 1111 atoms, 1068 bonds, 201 residues, 1 model selected > color sel pink > select #1.1/J 1111 atoms, 1068 bonds, 201 residues, 1 model selected > select #1.1/J 1111 atoms, 1068 bonds, 201 residues, 1 model selected > select #1.1/J 1111 atoms, 1068 bonds, 201 residues, 1 model selected > select #1.1/K 1110 atoms, 1068 bonds, 200 residues, 1 model selected > color sel plum > select #1.1/L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > color sel pink > select #1.2/I 1117 atoms, 1068 bonds, 207 residues, 1 model selected > color sel plum > select #1.2/J 1111 atoms, 1068 bonds, 201 residues, 1 model selected > color sel pink > select #1.2/K 1110 atoms, 1068 bonds, 200 residues, 1 model selected > color sel pink > color sel violet > color sel thistle > color sel light coral > color sel lavender > color sel violet > color sel plum > color sel light pink > color sel light green > color sel dark sea green > color sel light green > select #1.2/L 1115 atoms, 1068 bonds, 205 residues, 1 model selected > color sel dark sea green > color sel olive drab > color sel sea green > color sel dark sea green > color sel medium sea green > color sel sea green > color sel pale green > color sel dark sea green > color sel light green > color sel pale green > color sel light green > color sel dark sea green > color sel medium sea green > select /K 2220 atoms, 2136 bonds, 400 residues, 2 models selected > select /J /K /L 6672 atoms, 6408 bonds, 1212 residues, 2 models selected > color sel dark sea green > select /I 2234 atoms, 2136 bonds, 414 residues, 2 models selected > color sel medium sea green > color sel plum > color sel lavender > color sel plum > color sel light cyan > color sel honeydew > color sel yellow green > color sel green yellow > color sel light goldenrod yellow > color sel peach puff > color sel sea green > select /I /K 4454 atoms, 4272 bonds, 814 residues, 2 models selected > color sel sea green > select clear > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting soft > lighting full > save ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC complex.cxs"" > movie record > turn y 2 180 > wait 180 > movie encode /Users/jefflawton/Desktop/movie1.mp4 Movie saved to /Users/jefflawton/Desktop/movie1.mp4 > close session > open ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC active site.cxs"" format session opened ChimeraX session > select :344 16 atoms, 12 bonds, 4 residues, 1 model selected > select /G :344 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > close session > open ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC active site.cxs"" format session opened ChimeraX session > select /G :476 1 atom, 1 residue, 1 model selected > select /G :344 4 atoms, 3 bonds, 1 residue, 1 model selected > select /G :334 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select /G :177 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select /G :203 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select /G :201 12 atoms, 11 bonds, 1 residue, 1 model selected > label sel atoms text ""Lys-Carb 201"" > undo > select /G :201 12 atoms, 11 bonds, 1 residue, 1 model selected > ~label sel residues > label sel atoms text """" > select /G:201@CX 1 atom, 1 residue, 1 model selected > label sel text ""Carboxamide 201"" > select /G :204 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select /G:477@C 1 atom, 1 residue, 1 model selected > label sel text CO2 > label sel text ""{0.name} {0.number}{0.insertion_code}"" > label sel text """" > select /G:334@NZ 1 atom, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > label sel text ""Lys 334"" > label sel text """" > label sel text ""{0.name} {0.number}{0.insertion_code}"" > label height 0.7 > hide #1.2 models > show #1.2 models > select add #2 1 atom, 2 pseudobonds, 1 residue, 3 models selected > select subtract #2 1 atom, 1 residue, 1 model selected > show #2.1 models > save ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC active site (labels).cxs"" > movie record > turn y 2 180 > wait 180 > movie encode /Users/jefflawton/Desktop/movie1.mp4 Movie saved to /Users/jefflawton/Desktop/movie1.mp4 > hide #1.2 models > save /Users/jefflawton/Desktop/image1.png supersample 3 > close session > open ""/Users/jefflawton/Dropbox/EASTERN/321 Biochemistry II/Lecture > Notes/Chapter 20 Extras/8RUC active site (labels).cxs"" format session opened ChimeraX session > hide #2.1 models > movie record > turn y 2 180 > wait 180 > movie encode /Users/jefflawton/Desktop/movie1.mp4 Movie saved to /Users/jefflawton/Desktop/movie1.mp4 ===== Log before crash end ===== Log: 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 OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 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: Mac15,3 Model Number: MTL73LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.41.5 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7.1 (23H222) Kernel Version: Darwin 23.6.0 Time since boot: 18 days, 3 hours, 16 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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