Opened 5 months ago
Closed 5 months ago
#17875 closed defect (duplicate)
Crash on Mac waking from sleep
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Window Toolkit | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: macOS-15.4.1-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: Bus error Thread 0x000000032cf2f000 (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 0x000000032bf23000 (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 0x000000032af17000 (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 0x0000000329f0b000 (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 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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 0x0000000326ee7000 (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 0x0000000325edb000 (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 0x0000000324ecf000 (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 0x0000000323ec3000 (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 0x0000000322eb7000 (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 0x0000000321eab000 (most recent call 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"/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 0x00000001f1988c80 (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, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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Boot Volume File System Type: apfs Memory Module: LPDDR5, Hynix USB Device: USB31Bus USB Device: USB31Bus USB Device: USB31Bus Display: spdisplays_display, 1920 x 1080 (1080p FHD - Full High Definition), Main, MirrorOff, Online Model: MacBookPro18,3, BootROM 11881.101.1, proc 10:8:2 processors, 32 GB, SMC Graphics: Apple M1 Pro, Apple M1 Pro, Built-In AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4387), wl0: Feb 22 2025 01:26:18 version 20.130.16.0.8.7.195 FWID 01-81c38859 IO80211_driverkit-1475.34 "IO80211_driverkit-1475.34" Mar 9 2025 20:59:13 AirPort: Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd461x2/fold_igaa_rcsd461x2_model_0.cif Chain information for fold_igaa_rcsd461x2_model_0.cif #1 --- Chain | Description A | . B C | . Computing secondary structure > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd461x2_rcsf/fold_igaa_rcsd461x2_rcsf_model_0.cif Chain information for fold_igaa_rcsd461x2_rcsf_model_0.cif #2 --- Chain | Description A | . B C | . D | . Computing secondary structure > hide #2 models > hide #1 models > show #2 models > color #2 bychain > select #2/A:470-550 603 atoms, 606 bonds, 81 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2 to #1 & sel No 'to' model specified > matchmaker #1 to #2 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_igaa_rcsd461x2_rcsf_model_0.cif, chain A (#2) with fold_igaa_rcsd461x2_model_0.cif, chain A (#1), sequence alignment score = 409.3 RMSD between 81 pruned atom pairs is 0.324 angstroms; (across all 81 pairs: 0.324) > show #1 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #1 models > select #2/A:540 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:540 22 atoms, 20 bonds, 2 residues, 2 models selected > show sel & #2 atoms > show #1 models > hide #2 models > select /A:540 22 atoms, 20 bonds, 2 residues, 2 models selected > show sel & #1 atoms > show #2 models > hide #1 models > select /B:538,225,153,191,220 64 atoms, 56 bonds, 8 residues, 2 models selected > show sel & #2 atoms > show #1 models > hide #2 models > show sel & #1 atoms > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #1 models > show #1 models > select #1/A 5603 atoms, 5737 bonds, 711 residues, 1 model selected > color sel cornflower blue > select clear > select #1/B 3699 atoms, 3768 bonds, 461 residues, 1 model selected > ui tool show "Color Actions" > color sel hot pink > color sel plum > select #1/C 3699 atoms, 3768 bonds, 461 residues, 1 model selected > color sel cadet blue > select clear > hide #2 models > hide #1 models > show #1 models > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #1 models > set bgColor white > show #1 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #1 models > select #2/A:540 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/B:191 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B:220 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/B:225 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #2/B:191 24 atoms, 21 bonds, 3 residues, 1 model selected > select add #2/A:540@CA 25 atoms, 21 bonds, 4 residues, 1 model selected > select add #2/B:153 33 atoms, 28 bonds, 5 residues, 1 model selected > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsD461x2_RcsF.cxs" > select #2/C 3699 atoms, 3768 bonds, 461 residues, 1 model selected > ui tool show "Color Actions" > set bgColor honeydew > set bgColor white > color sel azure target acs > color sel honeydew target acs > color sel light green target acs > color sel pale green target acs > color sel light green target acs > color sel dark gray target acs > color sel pale green target acs > color sel light cyan target acs > color sel light green target acs > select #2/B 3699 atoms, 3768 bonds, 461 residues, 1 model selected > color sel peach puff target acs > color sel navajo white target acs > color sel moccasin target acs > color sel bisque target acs > color sel misty rose target acs > color sel peach puff target acs > color sel light goldenrod yellow target acs > color sel old lace target acs > color sel light pink target acs > color sel misty rose target acs > color sel bisque target acs > color sel moccasin target acs > color sel bisque target acs > color sel thistle target acs > color sel peach puff target acs > select #2/A 5603 atoms, 5737 bonds, 711 residues, 1 model selected > color sel thistle target acs > select #2/D 984 atoms, 1001 bonds, 134 residues, 1 model selected > color sel gray target acs > select clear > select #2/A:540 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel medium purple target acs > label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}" > select clear > select add #2/B:153 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/B:225 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #2/B:220 24 atoms, 21 bonds, 3 residues, 1 model selected > select add #2/B:191 32 atoms, 28 bonds, 4 residues, 1 model selected > ui tool show "Color Actions" > color sel orange target acs > color sel dark orange target acs > color sel orange target acs > label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}" > select clear > show #1 models > hide #!2 models > select #1/A 5603 atoms, 5737 bonds, 711 residues, 1 model selected > color sel light blue target acs > select #1/A:540@CA 1 atom, 1 residue, 1 model selected > select clear > select #1/A:540 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel cornflower blue target acs > select #1/B 3699 atoms, 3768 bonds, 461 residues, 1 model selected > color sel light pink target acs > select clear > select add #1/B:153 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1/B:225 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #1/B:220@CA 17 atoms, 14 bonds, 3 residues, 1 model selected > select add #1/B:191 25 atoms, 21 bonds, 4 residues, 1 model selected > color sel violet target acs > select clear > select #1/B:220 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel violet target acs > select clear > select add #1/B:153 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!2 models > hide #!2 models > select add #1/B:225 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #1/A:540 27 atoms, 24 bonds, 3 residues, 1 model selected > select add #1/B:220 35 atoms, 31 bonds, 4 residues, 1 model selected > select add #1/B:191 43 atoms, 38 bonds, 5 residues, 1 model selected > label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}" > select clear > show #!2 models Drag select of 56 atoms, 229 residues, 46 bonds > ~label sel residues > select #2/D:131 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #1 models > show #1 models > hide #1 models > select #2?A Expected an objects specifier or a keyword > select #2/A 5603 atoms, 5737 bonds, 711 residues, 1 model selected > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsD461x2_RcsF.cxs" > close session > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE- > NsrR/model/RpoE-NsrR.0.46.pdb Chain information for RpoE-NsrR.0.46.pdb #1 --- Chain | Description A | No description available B | No description available Computing secondary structure > color bychain > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_0.cif Chain information for fold_nsrr_rpoe_model_0.cif #2 --- Chain | Description A | . B | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_1.cif Chain information for fold_nsrr_rpoe_model_1.cif #3 --- Chain | Description A | . B | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_2.cif Chain information for fold_nsrr_rpoe_model_2.cif #4 --- Chain | Description A | . B | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_3.cif Chain information for fold_nsrr_rpoe_model_3.cif #5 --- Chain | Description A | . B | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_4.cif Chain information for fold_nsrr_rpoe_model_4.cif #6 --- Chain | Description A | . B | . Computing secondary structure > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna/fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif Chain information for fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif #7 --- Chain | Description A B | . C | . D | . E | . F | . G | . H | . I | . > select add #7 31862 atoms, 32543 bonds, 3921 residues, 1 model selected > hide sel atoms > show sel cartoons Computing secondary structure > select #2/A 1092 atoms, 1107 bonds, 141 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2-7 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_0.cif, chain B (#2), sequence alignment score = 907.7 RMSD between 89 pruned atom pairs is 0.447 angstroms; (across all 191 pairs: 20.111) Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_1.cif, chain B (#3), sequence alignment score = 889.1 RMSD between 90 pruned atom pairs is 0.465 angstroms; (across all 191 pairs: 19.665) Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_2.cif, chain B (#4), sequence alignment score = 916.7 RMSD between 89 pruned atom pairs is 0.433 angstroms; (across all 191 pairs: 19.763) Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_3.cif, chain B (#5), sequence alignment score = 889.1 RMSD between 87 pruned atom pairs is 0.475 angstroms; (across all 191 pairs: 20.684) Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_4.cif, chain B (#6), sequence alignment score = 917.3 RMSD between 89 pruned atom pairs is 0.433 angstroms; (across all 191 pairs: 20.441) Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7), sequence alignment score = 899.1 RMSD between 70 pruned atom pairs is 0.646 angstroms; (across all 190 pairs: 39.997) > hide #3 models > show #3 models > hide #1 models > hide #7 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > show #3 models > hide #3 models > ui tool show Matchmaker > select #2/A 1092 atoms, 1107 bonds, 141 residues, 1 model selected > matchmaker #3-7 to #2 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with fold_nsrr_rpoe_model_1.cif, chain A (#3), sequence alignment score = 691.7 RMSD between 125 pruned atom pairs is 0.432 angstroms; (across all 141 pairs: 5.993) Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with fold_nsrr_rpoe_model_2.cif, chain A (#4), sequence alignment score = 700.7 RMSD between 125 pruned atom pairs is 0.414 angstroms; (across all 141 pairs: 5.947) Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with fold_nsrr_rpoe_model_3.cif, chain A (#5), sequence alignment score = 685.7 RMSD between 123 pruned atom pairs is 0.503 angstroms; (across all 141 pairs: 5.951) Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with fold_nsrr_rpoe_model_4.cif, chain A (#6), sequence alignment score = 685.7 RMSD between 124 pruned atom pairs is 0.469 angstroms; (across all 141 pairs: 6.006) Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain G (#7), sequence alignment score = 685.7 RMSD between 110 pruned atom pairs is 0.636 angstroms; (across all 141 pairs: 6.185) > matchmaker #1 to #2 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with RpoE-NsrR.0.46.pdb, chain B (#1), sequence alignment score = 688.7 RMSD between 125 pruned atom pairs is 0.641 angstroms; (across all 141 pairs: 6.103) > show #3 models > show #4 models > show #5 models > show #6 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > show #7 models > hide #2 models > select #7/E 1519 atoms, 1543 bonds, 190 residues, 1 model selected > color sel cornflower blue > select clear > show #2 models > show #3 models > hide #3 models > hide #2 models > show #4 models > hide #4 models > show #5 models > hide #5 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #5 models > hide #5 models > show #6 models > hide #6 models > show #1 models > hide #7 models > show #7 models > hide #1 models > hide #7 models > show #3 models > show #4 models > show #5 models > hide #3 models > hide #4 models > hide #5 models Enter a PDB ID in the entry field > open 6jbq fromDatabase pdb format mmcif 6jbq title: CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA [more info...] Chain information for 6jbq #8 --- Chain | Description | UniProt A B | DNA-directed RNA polymerase subunit alpha | RPOA_ECOLI 1-329 C | DNA-directed RNA polymerase subunit beta | RPOB_ECOLI 1-1342 D | DNA-directed RNA polymerase subunit beta' | RPOC_ECOLI 1-1407 E | DNA-directed RNA polymerase subunit omega | RPOZ_ECOLI 1-91 F | ECF RNA polymerase sigma-E factor | RPOE_ECOLI 1-191 G | DNA (48-MER) | H | DNA (48-MER) | I | RNA (5'-R(*CP*UP*CP*GP*A)-3') | Non-standard residues in 6jbq #8 --- MG — magnesium ion ZN — zinc ion > open 1or7 fromDatabase pdb format mmcif Summary of feedback from opening 1or7 fetched from pdb --- warning | Atom CE has no neighbors to form bonds with according to residue template for MET /B:144 1or7 title: Crystal Structure of Escherichia coli sigmaE with the Cytoplasmic Domain of its Anti-sigma RseA [more info...] Chain information for 1or7 #9 --- Chain | Description | UniProt A B | RNA polymerase sigma-E factor | RPOE_ECOLI 1-191 C F | Sigma-E factor negative regulatory protein | RSEA_ECOLI 1-90 1or7 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| software_defined_assembly 37 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!8-9 atoms > show #!8-9 cartoons Drag select of 475 residues, 2 pseudobonds > color sel bychain > show #7 models > select #7/E 1519 atoms, 1543 bonds, 190 residues, 1 model selected > show #2 models > hide #7 models > select up 31862 atoms, 32543 bonds, 3921 residues, 1 model selected > select #2/A 1092 atoms, 1107 bonds, 141 residues, 1 model selected > show #7 models > hide #2 models > select #7/E 1519 atoms, 1543 bonds, 190 residues, 1 model selected > matchmaker #!8-9 to #7 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with 6jbq, chain F (#8), sequence alignment score = 876.9 RMSD between 156 pruned atom pairs is 1.135 angstroms; (across all 185 pairs: 1.567) Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with 1or7, chain A (#9), sequence alignment score = 870.6 RMSD between 59 pruned atom pairs is 0.408 angstroms; (across all 178 pairs: 36.626) > hide #!8 models > show #!8 models > hide #!8 models > hide #7 models > show #7 models > show #!8 models > hide #7 models > show #7 models > hide #!8 models > show #!8 models > hide #!9 models > hide #!8 models > hide #7 models > show #!8 models > show #7 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #!8 models > show #!8 models > hide #7 models > show #7 models > hide #!8 models > show #!9 models > hide #7 models > select #9/B/F 1947 atoms, 1863 bonds, 1 pseudobond, 339 residues, 2 models selected > delete atoms (#!9 & sel) > delete bonds (#!9 & sel) > ui tool show Matchmaker > select #7/E 1519 atoms, 1543 bonds, 190 residues, 1 model selected > show #7 models > matchmaker #!9 to #7 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with 1or7, chain A (#9), sequence alignment score = 870.6 RMSD between 59 pruned atom pairs is 0.408 angstroms; (across all 178 pairs: 36.626) > hide #!9 models > show #!9 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #7 models > show #2 models > show #7 models > select #7/E 1519 atoms, 1543 bonds, 190 residues, 1 model selected > matchmaker #1-6 to #7 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with RpoE-NsrR.0.46.pdb, chain A (#1), sequence alignment score = 899.1 RMSD between 70 pruned atom pairs is 0.646 angstroms; (across all 190 pairs: 39.997) Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with fold_nsrr_rpoe_model_0.cif, chain B (#2), sequence alignment score = 898.5 RMSD between 53 pruned atom pairs is 0.429 angstroms; (across all 190 pairs: 50.910) Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with fold_nsrr_rpoe_model_1.cif, chain B (#3), sequence alignment score = 873.3 RMSD between 64 pruned atom pairs is 0.339 angstroms; (across all 190 pairs: 50.319) Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with fold_nsrr_rpoe_model_2.cif, chain B (#4), sequence alignment score = 900.9 RMSD between 71 pruned atom pairs is 0.332 angstroms; (across all 190 pairs: 50.885) Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with fold_nsrr_rpoe_model_3.cif, chain B (#5), sequence alignment score = 879.9 RMSD between 6 pruned atom pairs is 1.532 angstroms; (across all 190 pairs: 34.202) Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with fold_nsrr_rpoe_model_4.cif, chain B (#6), sequence alignment score = 901.5 RMSD between 6 pruned atom pairs is 1.537 angstroms; (across all 190 pairs: 33.265) > hide #7 models > show #7 models > hide #!9 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #7 models > show #7 models > hide #2 models > show #2 models > hide #7 models > select add #2 4138 atoms, 4201 bonds, 522 residues, 2 models selected > color sel & #2 bychain > select #2/B 1527 atoms, 1551 bonds, 191 residues, 1 model selected > rainbow sel > show #!8 models > hide #!8 models > show #!9 models > show #6 models > hide #6 models > show #7 models > hide #2 models > hide #!9 models > select #7/E 1519 atoms, 1543 bonds, 190 residues, 1 model selected > rainbow sel > select clear > show #2 models > hide #2 models > show #2 models > hide #7 models > show #7 models > hide #2 models > show #!9 models > hide #7 models > select #9/A 1473 atoms, 1463 bonds, 1 pseudobond, 214 residues, 2 models selected > rainbow sel > select clear > show #7 models > hide #7 models > show #2 models > hide #!9 models > show #7 models > select #7/E 1519 atoms, 1543 bonds, 190 residues, 1 model selected > matchmaker #!8-9 to #7 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with 6jbq, chain F (#8), sequence alignment score = 876.9 RMSD between 156 pruned atom pairs is 1.135 angstroms; (across all 185 pairs: 1.567) Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7) with 1or7, chain A (#9), sequence alignment score = 870.6 RMSD between 59 pruned atom pairs is 0.408 angstroms; (across all 178 pairs: 36.626) > show #!9 models > hide #7 models > hide #2 models > show #7 models > hide #!9 models > show #!9 models > hide #7 models > show #7 models > hide #!9 models > show #!9 models > hide #7 models > show #7 models > hide #!9 models > show #!9 models > hide #!9 models > select clear > show #!9 models > show #2 models > hide #7 models > select #9/A:120-187 546 atoms, 551 bonds, 68 residues, 1 model selected > matchmaker #1-6 to #9 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1or7, chain A (#9) with RpoE-NsrR.0.46.pdb, chain A (#1), sequence alignment score = 318.7 RMSD between 64 pruned atom pairs is 0.531 angstroms; (across all 68 pairs: 1.615) Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_0.cif, chain B (#2), sequence alignment score = 319.6 RMSD between 63 pruned atom pairs is 0.468 angstroms; (across all 68 pairs: 2.300) Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_1.cif, chain B (#3), sequence alignment score = 324.4 RMSD between 64 pruned atom pairs is 0.429 angstroms; (across all 68 pairs: 2.533) Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_2.cif, chain B (#4), sequence alignment score = 318.7 RMSD between 64 pruned atom pairs is 0.349 angstroms; (across all 68 pairs: 2.870) Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_3.cif, chain B (#5), sequence alignment score = 324.4 RMSD between 64 pruned atom pairs is 0.502 angstroms; (across all 68 pairs: 2.315) Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_4.cif, chain B (#6), sequence alignment score = 322.3 RMSD between 64 pruned atom pairs is 0.390 angstroms; (across all 68 pairs: 1.306) > hide #2 models > select #9/C 563 atoms, 540 bonds, 97 residues, 1 model selected > color sel gray > select clear > show #2 models > hide #!9 models > show #!9 models > hide #2 models > select #9/A:120-187 546 atoms, 551 bonds, 68 residues, 1 model selected > show #2 models > hide #!9 models > show #3 models > hide #2 models > select #2/B#/B#4/B#5/B Expected an objects specifier or a keyword > select #2/B#3/B#4/B#5/B 6108 atoms, 6204 bonds, 764 residues, 4 models selected > select #2/B#3/B#4/B#5/B#6/B 7635 atoms, 7755 bonds, 955 residues, 5 models selected > show #2 models > show #4 models > show #5 models > show #6 models > rainbow sel Drag select of 5 residues > hide #3 models > hide #4 models > hide #5 models > hide #6 models > show #!9 models > hide #2 models > show #7 models > hide #!9 models > show #!8 models > hide #7 models > show #7 models > hide #7 models > select #2/B#3/B#4/B#5/B#6/B#8/F 9118 atoms, 9262 bonds, 1141 residues, 6 models selected > rainbow sel & #!8 Drag select of 7 residues > select #2/B#3/B#4/B#5/B#6/B#8/F 9118 atoms, 9262 bonds, 1141 residues, 6 models selected > show sel & #!8 surfaces > select #8/F 1483 atoms, 1507 bonds, 186 residues, 1 model selected > hide sel surfaces > show sel surfaces > show #!9 models > hide #!8 models > select #9/A 1473 atoms, 1463 bonds, 1 pseudobond, 214 residues, 2 models selected > show sel surfaces > show #7 models > show #!8 models > hide #7 models > hide #!8 models > show #2 models > hide #!9 models > show #3 models > show #4 models > show #5 models > show #6 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > show #!9 models > hide sel surfaces > hide #2 models > show #2 models > hide #!9 models > show #!9 models > show #3 models > show #4 models > show #5 models > hide #3 models > hide #4 models > hide #5 models > hide #2 models > ui tool show ESMFold > esmfold predict #1/A directory /Users/taic/Downloads/ChimeraX/ESMFold ESMFold Service Broken ## ESMFold Prediction Service Broken October 26, 2023 The ChimeraX ESMFold prediction service is down because Meta's prediction server has an SSL certificate problem. Meta is working on fixing it as described in this bug report https://github.com/facebookresearch/esm/discussions/627 and there is a ChimeraX ticket ChimeraX ticket debugging this problem. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10056 We do not have an estimate for when (if ever) the Meta sever will be working again. > show #!8 models > hide #!8 models > show #!8 models > show #7 models > hide #!9 models > hide #!8 models > show #!8 models > hide #!8 models > show #2 models > hide #7 models > show #!8 models > hide #2#!8 surfaces > hide #2 models > show #!9 models > open 1or7 fromDatabase pdb format mmcif Summary of feedback from opening 1or7 fetched from pdb --- warning | Atom CE has no neighbors to form bonds with according to residue template for MET /B:144 1or7 title: Crystal Structure of Escherichia coli sigmaE with the Cytoplasmic Domain of its Anti-sigma RseA [more info...] Chain information for 1or7 #10 --- Chain | Description | UniProt A B | RNA polymerase sigma-E factor | RPOE_ECOLI 1-191 C F | Sigma-E factor negative regulatory protein | RSEA_ECOLI 1-90 1or7 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| software_defined_assembly 37 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Drag select of 450 residues, 2 pseudobonds > color sel bychain > select clear > select #10/B/F 1947 atoms, 1863 bonds, 1 pseudobond, 339 residues, 2 models selected > delete atoms (#!10 & sel) > delete bonds (#!10 & sel) > select #10/A 1473 atoms, 1463 bonds, 1 pseudobond, 214 residues, 2 models selected > rainbow sel > hide #!9 models > select #8/F:1-110 841 atoms, 858 bonds, 106 residues, 1 model selected > matchmaker #!10 to #8 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6jbq, chain F (#8) with 1or7, chain A (#10), sequence alignment score = 487.6 RMSD between 84 pruned atom pairs is 0.815 angstroms; (across all 106 pairs: 5.890) > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > select #10/C 563 atoms, 540 bonds, 97 residues, 1 model selected > color sel gray > select clear > show #!8 models > show #2 models > select #8/F:1-110 841 atoms, 858 bonds, 106 residues, 1 model selected > matchmaker #1-6 to #8 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6jbq, chain F (#8) with RpoE-NsrR.0.46.pdb, chain A (#1), sequence alignment score = 505.6 RMSD between 83 pruned atom pairs is 0.778 angstroms; (across all 106 pairs: 10.486) Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_0.cif, chain B (#2), sequence alignment score = 506.8 RMSD between 83 pruned atom pairs is 0.756 angstroms; (across all 106 pairs: 18.674) Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_1.cif, chain B (#3), sequence alignment score = 506.2 RMSD between 83 pruned atom pairs is 0.769 angstroms; (across all 106 pairs: 15.065) Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_2.cif, chain B (#4), sequence alignment score = 506.2 RMSD between 83 pruned atom pairs is 0.734 angstroms; (across all 106 pairs: 18.352) Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_3.cif, chain B (#5), sequence alignment score = 503.2 RMSD between 83 pruned atom pairs is 0.754 angstroms; (across all 106 pairs: 18.529) Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_4.cif, chain B (#6), sequence alignment score = 506.2 RMSD between 83 pruned atom pairs is 0.768 angstroms; (across all 106 pairs: 18.847) > hide #!9 models > hide #!10 models > hide #2 models > show sel surfaces > hide sel surfaces > show #!10 models > hide #!8 models > show #!8 models > show #2 models > hide #!8 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #2 models > show #2 models > hide #!10 models > show #!10 models > hide #2 models > show #2 models > hide #!10 models > show #3 models > show #!8 models > hide #!8 models > show #!8 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #!8 models > hide #2 models > show #2 models > hide #3 models > show #4 models > hide #4 models > show #5 models > hide #2 models > show #2 models > show #6 models > hide #5 models > hide #2 models > show #!10 models > hide #6 models > show #2 models > hide #2 models > show #2 models > hide #!10 models > show #!10 models > hide #2 models > hide #!10 models > show #2 models > show #3 models > hide #2 models > show #2 models > show #4 models > hide #3 models > hide #2 models > hide #4 models > show #5 models > show #6 models > hide #5 models > show #2 models > hide #6 models > show #6 models > hide #2 models > show #!8 models > hide #6 models > show #6 models > hide #6 models > show #7 models > show #2 models > hide #!8 models > hide #7 models > show #7 models > ui tool show "Side View" > hide #2 models > show #3 models > show #4 models > hide #3 models > show #5 models > hide #4 models > show #6 models > hide #5 models > hide #7 models > show #7 models > hide #6 models > show #!10 models > hide #!10 models > show #6 models > hide #7 models > select add #10 2877 atoms, 2861 bonds, 1 pseudobond, 417 residues, 5 models selected > select subtract #10 841 atoms, 858 bonds, 106 residues, 2 models selected > show #!10 models > hide #6 models > show #6 models > hide #!10 models > show #5 models > hide #6 models > show #4 models > hide #5 models > hide #4 models > show #5 models > show #!10 models > hide #5 models > show #1 models > hide #!10 models > show #2 models > hide #1 models > hide #2 models > show #2 models > show #1 models > hide #2 models > select #8/F:1-110 841 atoms, 858 bonds, 106 residues, 1 model selected > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > select #1/A:8 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A 3065 atoms, 3089 bonds, 191 residues, 1 model selected > rainbow sel > show #2 models > hide #2 models > show #!9 models > hide #!9 models > show #!10 models > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE- > NsrR/model/RpoE-NsrR.0.46.pdb Chain information for RpoE-NsrR.0.46.pdb #11 --- Chain | Description A | No description available B | No description available Computing secondary structure > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE- > NsrR/model/RpoE-NsrR.0.44.pdb Chain information for RpoE-NsrR.0.44.pdb #12 --- Chain | Description A | No description available B | No description available Computing secondary structure > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE- > NsrR/model/RpoE-NsrR.0.437.pdb Chain information for RpoE-NsrR.0.437.pdb #13 --- Chain | Description A | No description available B | No description available Computing secondary structure > matchmaker #11-13 to #8 & sel No 'to' model specified > select #1/A 3065 atoms, 3089 bonds, 191 residues, 1 model selected > matchmaker #11-13 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with RpoE-NsrR.0.46.pdb, chain A (#11), sequence alignment score = 980.9 RMSD between 191 pruned atom pairs is 0.000 angstroms; (across all 191 pairs: 0.000) Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with RpoE-NsrR.0.44.pdb, chain A (#12), sequence alignment score = 980.9 RMSD between 191 pruned atom pairs is 0.688 angstroms; (across all 191 pairs: 0.688) Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with RpoE-NsrR.0.437.pdb, chain A (#13), sequence alignment score = 973.7 RMSD between 191 pruned atom pairs is 0.660 angstroms; (across all 191 pairs: 0.660) > hide #!10 models > select add #11 8348 atoms, 8411 bonds, 523 residues, 2 models selected > select add #12 13631 atoms, 13733 bonds, 855 residues, 3 models selected > select add #13 18914 atoms, 19055 bonds, 1187 residues, 4 models selected > delete atoms sel > delete bonds sel > select add #1 2218 atoms, 2233 bonds, 141 residues, 1 model selected > delete atoms sel > delete bonds sel > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE- > NsrR/model/RpoE-NsrR.0.46.pdb Chain information for RpoE-NsrR.0.46.pdb #1 --- Chain | Description A | No description available B | No description available Computing secondary structure > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_0.pdb Chain information for ranked_0.pdb #11 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_1.pdb Chain information for ranked_1.pdb #12 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_2.pdb Chain information for ranked_2.pdb #13 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_3.pdb Chain information for ranked_3.pdb #14 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_4.pdb Chain information for ranked_4.pdb #15 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_5.pdb Chain information for ranked_5.pdb #16 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_6.pdb Chain information for ranked_6.pdb #17 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_7.pdb Chain information for ranked_7.pdb #18 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_8.pdb Chain information for ranked_8.pdb #19 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_9.pdb Chain information for ranked_9.pdb #20 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_10.pdb Chain information for ranked_10.pdb #21 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_11.pdb Chain information for ranked_11.pdb #22 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_12.pdb Chain information for ranked_12.pdb #23 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_13.pdb Chain information for ranked_13.pdb #24 --- Chain | Description A | No description available B | No description available > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_14.pdb Chain information for ranked_14.pdb #25 --- Chain | Description A | No description available B | No description available Computing secondary structure > select #8/F:1-110 841 atoms, 858 bonds, 106 residues, 1 model selected > matchmaker #1,11-25 to #8 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6jbq, chain F (#8) with RpoE-NsrR.0.46.pdb, chain A (#1), sequence alignment score = 505.6 RMSD between 83 pruned atom pairs is 0.778 angstroms; (across all 106 pairs: 10.486) Matchmaker 6jbq, chain F (#8) with ranked_0.pdb, chain A (#11), sequence alignment score = 505.6 RMSD between 83 pruned atom pairs is 0.778 angstroms; (across all 106 pairs: 10.486) Matchmaker 6jbq, chain F (#8) with ranked_1.pdb, chain A (#12), sequence alignment score = 505.6 RMSD between 83 pruned atom pairs is 0.779 angstroms; (across all 106 pairs: 10.474) Matchmaker 6jbq, chain F (#8) with ranked_2.pdb, chain A (#13), sequence alignment score = 505.6 RMSD between 83 pruned atom pairs is 0.794 angstroms; (across all 106 pairs: 10.448) Matchmaker 6jbq, chain F (#8) with ranked_3.pdb, chain A (#14), sequence alignment score = 496.6 RMSD between 85 pruned atom pairs is 0.903 angstroms; (across all 106 pairs: 8.808) Matchmaker 6jbq, chain F (#8) with ranked_4.pdb, chain A (#15), sequence alignment score = 505.6 RMSD between 85 pruned atom pairs is 0.852 angstroms; (across all 106 pairs: 8.184) Matchmaker 6jbq, chain F (#8) with ranked_5.pdb, chain A (#16), sequence alignment score = 505.6 RMSD between 85 pruned atom pairs is 0.852 angstroms; (across all 106 pairs: 8.155) Matchmaker 6jbq, chain F (#8) with ranked_6.pdb, chain A (#17), sequence alignment score = 513.4 RMSD between 84 pruned atom pairs is 0.909 angstroms; (across all 106 pairs: 10.037) Matchmaker 6jbq, chain F (#8) with ranked_7.pdb, chain A (#18), sequence alignment score = 516.4 RMSD between 86 pruned atom pairs is 0.856 angstroms; (across all 106 pairs: 9.728) Matchmaker 6jbq, chain F (#8) with ranked_8.pdb, chain A (#19), sequence alignment score = 517 RMSD between 85 pruned atom pairs is 0.813 angstroms; (across all 106 pairs: 8.015) Matchmaker 6jbq, chain F (#8) with ranked_9.pdb, chain A (#20), sequence alignment score = 506.8 RMSD between 86 pruned atom pairs is 0.790 angstroms; (across all 106 pairs: 9.591) Matchmaker 6jbq, chain F (#8) with ranked_10.pdb, chain A (#21), sequence alignment score = 497.8 RMSD between 82 pruned atom pairs is 0.931 angstroms; (across all 106 pairs: 10.773) Matchmaker 6jbq, chain F (#8) with ranked_11.pdb, chain A (#22), sequence alignment score = 517.6 RMSD between 83 pruned atom pairs is 1.032 angstroms; (across all 106 pairs: 9.232) Matchmaker 6jbq, chain F (#8) with ranked_12.pdb, chain A (#23), sequence alignment score = 497.8 RMSD between 80 pruned atom pairs is 0.799 angstroms; (across all 106 pairs: 14.376) Matchmaker 6jbq, chain F (#8) with ranked_13.pdb, chain A (#24), sequence alignment score = 509.8 RMSD between 76 pruned atom pairs is 0.805 angstroms; (across all 106 pairs: 16.260) Matchmaker 6jbq, chain F (#8) with ranked_14.pdb, chain A (#25), sequence alignment score = 496.6 RMSD between 88 pruned atom pairs is 0.801 angstroms; (across all 106 pairs: 11.350) > hide #12 models > hide #13 models > hide #14 models > hide #15 models > hide #16 models > hide #17 models > hide #18 models > hide #19 models > hide #20 models > hide #21 models > hide #22 models > hide #23 models > hide #24 models > hide #25 models > show #!8 models > show #!10 models > hide #!8 models > hide #!10 models > select #11-#25/A Expected an objects specifier or a keyword > select #11/A-#25/A Expected an objects specifier or a keyword > select #11/A#25/A 6130 atoms, 6178 bonds, 382 residues, 2 models selected > rainbow sel & #11 > select add #11 8348 atoms, 8411 bonds, 523 residues, 2 models selected > hide #1 models > show #1 models > hide #1 models > show #12 models > show #13 models > show #14 models > hide #14 models > hide #12 models > hide #13 models > show #14 models > select #14/A#25/A 6130 atoms, 6178 bonds, 382 residues, 2 models selected > select #14/A 3065 atoms, 3089 bonds, 191 residues, 1 model selected > rainbow sel > hide #11 models > show #11 models > hide #11 models > show #15 models > hide #15 models > hide #14 models > show #15 models > hide #15 models > show #11 models > show #15 models > show #16 models > hide #15 models > show #15 models > hide #16 models > show #17 models > hide #15 models > hide #11 models > show #11 models > show #15 models > show #18 models > hide #11 models > hide #15 models > show #19 models > hide #18 models > hide #17 models > show #20 models > hide #19 models > show #21 models > hide #20 models > show #22 models > hide #21 models > show #23 models > hide #22 models > show #11 models > hide #11 models > show #24 models > show #25 models > hide #23 models > hide #24 models > select add #11 8348 atoms, 8411 bonds, 523 residues, 2 models selected > select add #12 13631 atoms, 13733 bonds, 855 residues, 3 models selected > select add #13 18914 atoms, 19055 bonds, 1187 residues, 4 models selected > select add #14 21132 atoms, 21288 bonds, 1328 residues, 4 models selected > select add #15 26415 atoms, 26610 bonds, 1660 residues, 5 models selected > select add #16 31698 atoms, 31932 bonds, 1992 residues, 6 models selected > select add #17 36981 atoms, 37254 bonds, 2324 residues, 7 models selected > select add #18 42264 atoms, 42576 bonds, 2656 residues, 8 models selected > select add #19 47547 atoms, 47898 bonds, 2988 residues, 9 models selected > select add #20 52830 atoms, 53220 bonds, 3320 residues, 10 models selected > select add #21 58113 atoms, 58542 bonds, 3652 residues, 11 models selected > select add #22 63396 atoms, 63864 bonds, 3984 residues, 12 models selected > select add #23 68679 atoms, 69186 bonds, 4316 residues, 13 models selected > select add #24 73962 atoms, 74508 bonds, 4648 residues, 14 models selected > select add #25 79245 atoms, 79830 bonds, 4980 residues, 15 models selected > delete atoms (#25 & sel) > delete bonds (#25 & sel) > show #11 models > show #12 models > show #13 models > show #14 models > show #15 models > show #16 models > show #17 models > show #18 models > show #19 models > show #20 models > show #21 models > show #22 models > show #23 models > show #24 models > hide #11 models > hide #12 models > show #12 models > hide #14 models > show #14 models > hide #14 models > show #14 models > hide #14 models > hide #18 models > show #18 models > hide #17 models > hide #21 models > delete atoms (#12-13,15-16,18-20,22-24 & sel) > delete bonds (#12-13,15-16,18-20,22-24 & sel) > show #11 models > show #14 models > show #!10 models > hide #11 models > hide #!10 models > show #17 models > show #!10 models > hide #14 models > hide #!10 models > show #21 models > hide #17 models > show #17 models > show #14 models > delete atoms (#14,17,21 & sel) > delete bonds (#14,17,21 & sel) > show #1 models > show #!10 models > hide #!10 models > select #1/A 3065 atoms, 3089 bonds, 191 residues, 1 model selected > rainbow sel > show #2 models > hide #1 models > show #!10 models > hide #2 models > show #1 models > hide #!10 models > show #!10 models > hide #!10 models > show #2 models > hide #1 models > show #!10 models > hide #2 models > show #1 models > hide #1 models > show #1 models > hide #!10 models > show #!10 models > show #2 models > hide #1 models > hide #!10 models > show #7 models > hide #2 models > select ::name="CYS" 598 atoms, 505 bonds, 93 residues, 11 models selected > select clear > select add #7/G:91 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #7/G:96 12 atoms, 10 bonds, 2 residues, 1 model selected > select add #7/G:102 18 atoms, 15 bonds, 3 residues, 1 model selected > color sel yellow > show sel atoms > style sel ball Changed 18 atom styles > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_0.cif Chain information for fold_nsrrx2_rpoe_model_0.cif #12 --- Chain | Description A B | . C | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_1.cif Chain information for fold_nsrrx2_rpoe_model_1.cif #13 --- Chain | Description A B | . C | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_2.cif Chain information for fold_nsrrx2_rpoe_model_2.cif #14 --- Chain | Description A B | . C | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_3.cif Chain information for fold_nsrrx2_rpoe_model_3.cif #15 --- Chain | Description A B | . C | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_4.cif Chain information for fold_nsrrx2_rpoe_model_4.cif #16 --- Chain | Description A B | . C | . Computing secondary structure > show #2 models > hide #7 models > select #2/B:1-120 950 atoms, 968 bonds, 120 residues, 1 model selected > ui tool show Matchmaker > matchmaker #12-16 to #2 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with fold_nsrrx2_rpoe_model_0.cif, chain C (#12), sequence alignment score = 549.2 RMSD between 85 pruned atom pairs is 0.293 angstroms; (across all 119 pairs: 10.408) Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with fold_nsrrx2_rpoe_model_1.cif, chain C (#13), sequence alignment score = 546.2 RMSD between 85 pruned atom pairs is 0.267 angstroms; (across all 119 pairs: 6.508) Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with fold_nsrrx2_rpoe_model_2.cif, chain C (#14), sequence alignment score = 570.4 RMSD between 83 pruned atom pairs is 0.357 angstroms; (across all 119 pairs: 18.762) Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with fold_nsrrx2_rpoe_model_3.cif, chain C (#15), sequence alignment score = 566.8 RMSD between 91 pruned atom pairs is 0.478 angstroms; (across all 119 pairs: 10.674) Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with fold_nsrrx2_rpoe_model_4.cif, chain C (#16), sequence alignment score = 569.8 RMSD between 80 pruned atom pairs is 0.319 angstroms; (across all 119 pairs: 18.622) > hide #13 models > hide #14 models > hide #15 models > hide #16 models > hide #2 models > show #2 models > hide #2 models > color #12 bychain > hide #12 models > show #12 models > show #2 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #2 models > show #13 models > show #14 models > show #15 models > show #16 models > color #12-16 bychain > hide #13 models > hide #14 models > show #13 models > hide #15 models > hide #16 models > show #2 models > hide #13 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #2 models > show #13 models > hide #12 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #13 models > show #12 models > hide #2 models > show #2 models > hide #2 models > show #13 models > hide #12 models > show #14 models > hide #13 models > show #!10 models Drag select of 1 residues > hide #!10 models > show #15 models > hide #14 models > show #2 models > hide #2 models > show #16 models > hide #15 models > show #2 models > hide #2 models > show #!10 models > hide #16 models > show #2 models > hide #!10 models > show #12 models > hide #2 models > show #!10 models > hide #12 models > show #2 models > hide #2 models > show #11 models > hide #!10 models > hide #11 models > show #11 models > show #2 models > hide #11 models > show #!10 models > hide #!10 models > show #12 models > hide #2 models > show #13 models > hide #12 models > show #!10 models > hide #13 models > select ((#10/A & ::polymer_type>0 ) & ((#10/C & ::polymer_type>0 ) :0 ) & ((#10/A & ::polymer_type>0 ) : interfaces select #10/A & ::polymer_type>0 contacting #10/C & > ::polymer_type>0 areaCutoff 0 bothSides true 98 contacting residues > select (#10/A & ::polymer_type>0 ) & ((#10/C & ::polymer_type>0 ) : show sel atoms > show #2 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #2 models > show #2 models > hide #!10 models > show #3 models > show #4 models > hide #3 models > hide #2 models > show #5 models > hide #4 models > show #12 models > hide #5 models > select #12/C 1519 atoms, 1543 bonds, 190 residues, 1 model selected > rainbow sel > show #13 models > hide #12 models > select #13/C 1519 atoms, 1543 bonds, 190 residues, 1 model selected > rainbow sel > show #!10 models > hide #13 models > show #13 models > hide #!10 models > show #14 models > hide #13 models > show #15 models > hide #14 models > show #16 models > hide #15 models > select #16/C 1519 atoms, 1543 bonds, 190 residues, 1 model selected > rainbow sel > show #!10 models > hide #!10 models > show #!10 models > hide #16 models > show #16 models > hide #!10 models > show #!10 models > hide #16 models > show #16 models > hide #!10 models > show #!10 models > hide #16 models > show #16 models > hide #!10 models > select clear > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_summary_confidences_0.json Failed opening file /Users/taic/Library/CloudStorage/OneDrive- NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_summary_confidences_0.json: Opening an AlphaFold PAE file requires first opening the predicted atomic model. Did not find an open atomic model from the same directory. If the atomic model is already open choose it using menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command structure option, for example open /Users/taic/Library/CloudStorage/OneDrive- NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_summary_confidences_0.json structure #1 If you are trying to open a JSON file that is not AlphaFold PAE data then you need to specify the specific JSON format such as open mole_channels.json format mole > show #!10 models > hide #16 models > show #16 models > hide #!10 models > select #16/C 1519 atoms, 1543 bonds, 190 residues, 1 model selected > show sel surfaces > hide sel surfaces > show #12 models > hide #!16 models > select #12/C 1519 atoms, 1543 bonds, 190 residues, 1 model selected > show sel surfaces > hide sel surfaces > show #!10 models > hide #!12 models > show #!10 surfaces > hide #!10 surfaces > show #11 models > hide #11 models > hide #!10 models > show #!12 models > show sel surfaces > select clear > hide #!12 surfaces > show #!12 surfaces > show #13 models > hide #!12 models > show #13 surfaces > hide #!13 surfaces > show #!13 surfaces > hide #!13 surfaces > show #!12 models > hide #!13 models > hide #!12 models > show #!12 models > hide #!12 surfaces > select #12/A 1092 atoms, 1107 bonds, 141 residues, 1 model selected > ui tool show Matchmaker > matchmaker #14-15#!13,16 to #12 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_rpoe_model_2.cif, chain A (#14), sequence alignment score = 707.3 RMSD between 136 pruned atom pairs is 0.403 angstroms; (across all 141 pairs: 0.756) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_rpoe_model_3.cif, chain A (#15), sequence alignment score = 714.5 RMSD between 137 pruned atom pairs is 0.403 angstroms; (across all 141 pairs: 0.863) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_rpoe_model_1.cif, chain A (#13), sequence alignment score = 714.5 RMSD between 136 pruned atom pairs is 0.420 angstroms; (across all 141 pairs: 0.746) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_rpoe_model_4.cif, chain A (#16), sequence alignment score = 707.3 RMSD between 135 pruned atom pairs is 0.443 angstroms; (across all 141 pairs: 0.785) > show #!13 models > hide #!12 models > show #14 models > hide #!13 models > show #15 models > hide #14 models > show #!16 models > hide #15 models > show #!12 models > show #14 models > show #!13 models > show #15 models > hide #!13 models > hide #14 models > hide #15 models > hide #!16 models > show #!13 models > hide #!12 models > show #!12 models > show #14 models > hide #!13 models > hide #!12 models > show #15 models > hide #14 models > show #!16 models > hide #15 models > hide #!16 models > show #2 models > show #!12 models > hide #2 models > select clear > show #!10 models > hide #!12 models > hide #!10 models > show #!8 models > show #!12 models > hide #!8 models > show #!13 models > hide #!13 models > select ::name="CYS" 808 atoms, 680 bonds, 128 residues, 16 models selected > show #!8 models > hide #!12 models > select clear > select #6/F Nothing selected > show #!8 surfaces > hide #!8 surfaces > select #8/F 1483 atoms, 1507 bonds, 186 residues, 1 model selected > show sel surfaces > select clear > hide #!8 surfaces > select (#8/F & ::polymer_type>0 ) & ((#8/G#8/H & ::polymer_type>0 ) : show sel atoms > style (#!8 & sel) ball Changed 376 atom styles > show sel surfaces > hide sel surfaces > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6jbq_F SES surface #8.4: minimum, -14.34, mean -1.22, maximum 10.80 To also show corresponding color key, enter the above coulombic command and add key true > select #8/F 1483 atoms, 1507 bonds, 186 residues, 1 model selected > coulombic sel Coulombic values for 6jbq_F SES surface #8.4: minimum, -14.34, mean -1.22, maximum 10.80 To also show corresponding color key, enter the above coulombic command and add key true > show #!12 models > hide #!8 models > coulombic #!12 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2: minimum, -15.92, mean -0.58, maximum 9.52 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3: minimum, -23.57, mean -0.56, maximum 12.88 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1: minimum, -22.04, mean -1.05, maximum 12.16 To also show corresponding color key, enter the above coulombic command and add key true > coulombic #!12 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2: minimum, -15.92, mean -0.58, maximum 9.52 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3: minimum, -23.57, mean -0.56, maximum 12.88 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1: minimum, -22.04, mean -1.05, maximum 12.16 To also show corresponding color key, enter the above coulombic command and add key true > hide #!12 surfaces > coulombic #!12 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2: minimum, -15.92, mean -0.58, maximum 9.52 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3: minimum, -23.57, mean -0.56, maximum 12.88 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1: minimum, -22.04, mean -1.05, maximum 12.16 To also show corresponding color key, enter the above coulombic command and add key true > show #!10 models > hide #!12 models > coulombic #!10 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1or7_A SES surface #10.2: minimum, -20.54, mean -1.07, maximum 9.07 Coulombic values for 1or7_C SES surface #10.3: minimum, -18.13, mean -4.40, maximum 6.24 To also show corresponding color key, enter the above coulombic command and add key true > hide #!10 surfaces > show #!8 models > hide #!10 models > hide sel surfaces > show #!10 models > hide #!8 models > show #2 models > hide #!10 models > show #!12 models > hide #2 models > hide #!12 surfaces > coulombic #!12 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2: minimum, -15.92, mean -0.58, maximum 9.52 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3: minimum, -23.57, mean -0.56, maximum 12.88 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1: minimum, -22.04, mean -1.05, maximum 12.16 To also show corresponding color key, enter the above coulombic command and add key true > coulombic #!12 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2: minimum, -15.92, mean -0.58, maximum 9.52 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3: minimum, -23.57, mean -0.56, maximum 12.88 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1: minimum, -22.04, mean -1.05, maximum 12.16 To also show corresponding color key, enter the above coulombic command and add key true > hide #!12 surfaces > coulombic #!12 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2: minimum, -15.92, mean -0.58, maximum 9.52 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3: minimum, -23.57, mean -0.56, maximum 12.88 Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1: minimum, -22.04, mean -1.05, maximum 12.16 To also show corresponding color key, enter the above coulombic command and add key true > hide #!12 surfaces > show #!13 models > hide #!12 models > coulombic #!13 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_nsrrx2_rpoe_model_1.cif_A SES surface #13.1: minimum, -16.22, mean -0.58, maximum 10.51 Coulombic values for fold_nsrrx2_rpoe_model_1.cif_B SES surface #13.2: minimum, -17.04, mean -0.57, maximum 9.45 Coulombic values for fold_nsrrx2_rpoe_model_1.cif_C SES surface #13.3: minimum, -14.19, mean -1.40, maximum 9.93 To also show corresponding color key, enter the above coulombic command and add key true > hide #!13 surfaces > show #14 models > hide #!13 models > show #!8 models > hide #14 models > show #!10 models > hide #!8 models > show #!12 models > hide #!10 models > show #!13 models > show #14 models > show #15 models > show #!16 models > hide #!13 models > hide #14 models > hide #15 models > hide #!16 models > show #!13 models > hide #!12 models > show #!12 models > hide #!13 models > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_0.cif Chain information for fold_nsrrx2_model_0.cif #17 --- Chain | Description A B | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_1.cif Chain information for fold_nsrrx2_model_1.cif #18 --- Chain | Description A B | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_2.cif Chain information for fold_nsrrx2_model_2.cif #19 --- Chain | Description A B | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_3.cif Chain information for fold_nsrrx2_model_3.cif #20 --- Chain | Description A B | . > open /Users/taic/Library/CloudStorage/OneDrive- > NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_4.cif Chain information for fold_nsrrx2_model_4.cif #21 --- Chain | Description A B | . Computing secondary structure > hide #!12 models > show #!12 models > select #12/A 1092 atoms, 1107 bonds, 141 residues, 1 model selected > ui tool show Matchmaker > matchmaker #17-21 to #12 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_model_0.cif, chain A (#17), sequence alignment score = 695.9 RMSD between 121 pruned atom pairs is 0.386 angstroms; (across all 141 pairs: 2.113) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_model_1.cif, chain A (#18), sequence alignment score = 678.5 RMSD between 123 pruned atom pairs is 0.411 angstroms; (across all 141 pairs: 1.724) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_model_2.cif, chain A (#19), sequence alignment score = 692.9 RMSD between 122 pruned atom pairs is 0.358 angstroms; (across all 141 pairs: 2.052) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_model_3.cif, chain B (#20), sequence alignment score = 692.9 RMSD between 123 pruned atom pairs is 0.360 angstroms; (across all 141 pairs: 1.914) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrrx2_model_4.cif, chain A (#21), sequence alignment score = 695.3 RMSD between 122 pruned atom pairs is 0.343 angstroms; (across all 141 pairs: 1.961) > hide #17 models > hide #18 models > show #17 models > hide #!12 models > hide #19 models > hide #20 models > hide #21 models > color #17 bychain > show #!13 models > show #!12 models > hide #!13 models > select clear > hide #17 models > show #!13 models > hide #!12 models > show #14 models > hide #!13 models > select #14/C#15/C#16/C 4557 atoms, 4629 bonds, 570 residues, 3 models selected > show #15 models > show #!16 models > rainbow sel > select clear > show #!10 models > hide #14 models > hide #!16 models > hide #15 models > show #15 models > hide #!10 models > hide #15 models > select add #18 2184 atoms, 2214 bonds, 282 residues, 1 model selected > select add #19 4368 atoms, 4428 bonds, 564 residues, 2 models selected > select add #20 6552 atoms, 6642 bonds, 846 residues, 3 models selected > select add #21 8736 atoms, 8856 bonds, 1128 residues, 4 models selected > show #18 models > show #19 models > show #20 models > hide #20 models > show #20 models > show #21 models > delete atoms sel > delete bonds sel > show #!12 models > show #!13 models > hide #!12 models > show #14 models > hide #!13 models > show #15 models > hide #14 models > show #!16 models > hide #15 models > show #!8 models > hide #!8 models > show #!12 models > hide #!16 models > show #2 models > hide #2 models > select #12/A 1092 atoms, 1107 bonds, 141 residues, 1 model selected > matchmaker #2-6 to #12 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrr_rpoe_model_0.cif, chain A (#2), sequence alignment score = 685.7 RMSD between 124 pruned atom pairs is 0.497 angstroms; (across all 141 pairs: 6.290) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrr_rpoe_model_1.cif, chain A (#3), sequence alignment score = 710.9 RMSD between 134 pruned atom pairs is 0.560 angstroms; (across all 141 pairs: 1.076) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrr_rpoe_model_2.cif, chain A (#4), sequence alignment score = 700.1 RMSD between 134 pruned atom pairs is 0.596 angstroms; (across all 141 pairs: 1.018) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrr_rpoe_model_3.cif, chain A (#5), sequence alignment score = 718.1 RMSD between 129 pruned atom pairs is 0.523 angstroms; (across all 141 pairs: 1.401) Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with fold_nsrr_rpoe_model_4.cif, chain A (#6), sequence alignment score = 718.1 RMSD between 134 pruned atom pairs is 0.617 angstroms; (across all 141 pairs: 1.130) > show #2 models > hide #!12 models > show #3 models > hide #2 models > show #2 models > hide #3 models > show #!8 models > hide #!8 models > show #11 models > hide #2 models > show #!12 models > hide #11 models > select clear > show #2 models > hide #!12 models > show #!12 models > hide #2 models > show #2 models > hide #!12 models > show #!12 models > hide #2 models > show #!13 models > hide #!12 models > show #14 models > hide #!13 models > show #15 models > hide #14 models > show #!16 models > hide #15 models > show #17 models > hide #!16 models > show #!12 models > show #!13 models > show #14 models > show #15 models > show #!16 models > show #2 models > hide #!13 models > hide #14 models > hide #15 models > hide #!16 models > hide #17 models > hide #!12 models > show #!12 models > hide #!12 models > show #17 models > hide #17 models > show #!12 models > hide #2 models > show #2 models > hide #!12 models > show #!12 models > hide #2 models > show #2 models > show #!13 models > hide #!12 models > hide #2 models > show #!12 models > hide #!13 models > show #!13 models > hide #!12 models > show #!12 models > hide #!13 models > show #11 models > hide #11 models > show #!13 models > hide #!12 models > show #14 models > hide #!13 models > show #!12 models > hide #14 models > show #14 models > hide #!12 models > show #!13 models > hide #14 models > show #17 models > hide #!13 models > show #!13 models > hide #17 models > show #2 models > hide #!13 models > show #!13 models > hide #2 models > show #2 models > hide #!13 models > show #!12 models > hide #2 models > show #!13 models > hide #!12 models > select #13/C:124-190 547 atoms, 552 bonds, 67 residues, 1 model selected > ui tool show Matchmaker > matchmaker #!8 to #13 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nsrrx2_rpoe_model_1.cif, chain C (#13) with 6jbq, chain F (#8), sequence alignment score = 313.7 RMSD between 66 pruned atom pairs is 0.882 angstroms; (across all 66 pairs: 0.882) > show #!8 models > hide #!13 models > show #!12 models > show #!13 models > hide #!12 models > hide #!8 models > show #!8 models > hide #!13 models > select #8/D 10334 atoms, 10485 bonds, 14 pseudobonds, 1338 residues, 3 models selected > color (#!8 & sel) light gray > select clear > select #8/D 10334 atoms, 10485 bonds, 14 pseudobonds, 1338 residues, 3 models selected > ui tool show "Color Actions" > color sel gainsboro target acs > color sel cornsilk target acs > color sel antique white target acs > color sel beige target acs > color sel antique white target acs > color sel pale goldenrod target acs > color sel antique white target acs > select clear > select #8/C 10320 atoms, 10485 bonds, 1 pseudobond, 1312 residues, 2 models selected > color sel light cyan target acs > color sel lavender target acs > color sel pale goldenrod target acs > color sel lavender target acs > color sel azure target acs > color sel honeydew target acs > select clear > select #8/C 10320 atoms, 10485 bonds, 1 pseudobond, 1312 residues, 2 models selected > color sel light cyan target acs > select clear > select #8/F 1483 atoms, 1507 bonds, 186 residues, 1 model selected > hide sel atoms > select #8/B:204 9 atoms, 8 bonds, 1 residue, 1 model selected > show #!13 models > hide #!8 models > show #!8 models > hide #!13 models > show #!13 models > hide #!8 models > show #14 models > hide #!13 models > show #15 models > hide #14 models > show #!16 models > hide #15 models > show #!12 models > hide #!16 models > show #!8 models > hide #!12 models > show #!13 models > hide #!8 models > show #!12 models > hide #!13 models > show #14 models > hide #!12 models > show #!13 models > show #15 models > hide #!13 models > show #!13 models > hide #14 models > hide #15 models > show #14 models > hide #!13 models > show #!13 models > show #!12 models > hide #14 models > hide #!13 models > show #!13 models > hide #!12 models > show #!8 models > hide #!13 models > show #!12 models > hide #!8 models > show #!13 models > hide #!12 models > show #15 models > hide #!13 models > show #!16 models > hide #15 models > hide #!16 models > show #!13 models > show #14 models > hide #14 models > show #!8 models > hide #!13 models > show #!12 models > hide #!8 models > show #!8 models > hide #!12 models > show #!13 models > hide #!8 models > show #!8 models > hide #!8 models > show #!12 models > hide #!12 models > show #!12 models > hide #!13 models > show #7 models > hide #!12 models > show #!12 models > hide #7 models > show #7 models > hide #7 models > show #!13 models > show #7 models > hide #7 models > hide #!12 models > show #7 models > show #!8 models > hide #7 models > show #!12 models > hide #!13 models > hide #!8 models > show #!13 models > hide #!12 models > show #!12 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!12 models > show #!8 models > hide #!13 models > show #!13 models > hide #!8 models > show #!8 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!8 models > show #!8 models > hide #!13 models > show #!13 models > hide #!8 models > show #!8 models > hide #!13 models > show #!13 models > hide #!8 models > show #!12 models > hide #!13 models > show #14 models > hide #!12 models > show #15 models > hide #14 models > show #!16 models > hide #15 models > show #!13 models > hide #!16 models > show #!8 models > hide #!13 models > show #!12 models > hide #!8 models > show #14 models > hide #!12 models > show #!16 models > hide #14 models > show #17 models > hide #!16 models > show #!16 models > hide #17 models > show #!12 models > hide #!16 models > show #!13 models > hide #!12 models > show #!8 models > hide #!13 models > show #!13 models > hide #!8 models > show #!12 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!12 models > show #!12 models > hide #!13 models > show #!13 models > hide #!12 models > show #!8 models > hide #!13 models > show #!10 models > hide #!8 models > select #10 2036 atoms, 2003 bonds, 1 pseudobond, 311 residues, 3 models selected > hide sel atoms > select clear Drag select of 11 residues > select #10/A:120 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > show #!13 models > hide #!10 models > show #!10 models > hide #!10 models > show #!8 models > hide #!13 models > show #!13 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!13 models > show #!13 models > show #!12 models > hide #!8 models > hide #!13 models > show #14 models > hide #!12 models > hide #14 models > show #!13 models > show #!16 models > hide #!13 models > hide #!16 models > show #!13 models > show #!12 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!12 models > show #14 models > hide #!13 models > show #!16 models > hide #14 models > show #17 models > hide #!16 models > show #!12 models > hide #17 models > select #12/C:120-160 332 atoms, 334 bonds, 41 residues, 1 model selected > ui tool show Matchmaker > matchmaker #!8 to #12 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain C (#12) with 6jbq, chain F (#8), sequence alignment score = 194.6 RMSD between 41 pruned atom pairs is 0.873 angstroms; (across all 41 pairs: 0.873) > show #!8 models > hide #!12 models > show #!13 models > show #!12 models > hide #!8 models > select clear > hide #!13 models > show #!8 models > hide #!8 models > show #!8 models > hide #!12 models > show #!12 models > hide #!8 models > show #!8 models > hide #!12 models > show #!12 models > hide #!8 models > show #!8 models > hide #!12 models > show #!12 models > hide #!8 models > show #!13 models > hide #!12 models > show #14 models > hide #!13 models > show #!12 models > hide #14 models > show #17 models > hide #!12 models > show #!12 models > hide #17 models > show #!13 models > hide #!12 models > show #!12 models > show #14 models > hide #!13 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #14 models > show #!8 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!8 models > show #17 models > hide #!12 models > show #!12 models > hide #17 models > show #!8 models > hide #!12 models > show #!12 models > hide #!8 models > show #!8 models > hide #!12 models > show #!13 models > hide #!8 models > show #14 models > hide #!13 models > show #17 models > hide #14 models > show #!12 models > hide #17 models > show #17 models > show #!8 models > hide #17 models > hide #!12 models > show #!10 models > hide #!8 models > hide #!10 models > show #!12 models > show #!8 models > hide #!12 models > select #8/I 102 atoms, 113 bonds, 5 residues, 1 model selected > color sel dark sea green target acs > color sel medium purple target acs > color sel olive target acs > select #8/C:499 6 atoms, 5 bonds, 1 residue, 1 model selected > show #!12 models > hide #!8 models > show #17 models > hide #!12 models > show #2 models > hide #17 models > show #17 models > hide #2 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/NsrR_RpoE.cxs" > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/Fig6C.NsrRx2.png" width 600 height > 487 supersample 4 transparentBackground true > show #!12 models > hide #17 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/Fig6D.NsrRx2_RpoE.png" width 600 > height 487 supersample 4 transparentBackground true > show #!8 models > hide #!12 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/FigS1B.1OR7zoomin.png" width 600 > height 487 supersample 4 transparentBackground true > show #!10 models > hide #!8 models > select #10/C 563 atoms, 540 bonds, 97 residues, 1 model selected > color (#!10 & sel) light gray > select clear > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/FigS1C.RpoE_RseA.1OR7.png" width 600 > height 487 supersample 4 transparentBackground true > show #!13 models > hide #!10 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/FigS1A.NsrR_RpoE.AF3.png" width 600 > height 487 supersample 4 transparentBackground true > show #14 models > hide #!13 models > show #!13 models > hide #14 models > show #14 models > hide #!13 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/FigS1F.NsrRx2_RpoE-2.png" width 600 > height 487 supersample 4 transparentBackground true > show #15 models > hide #14 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/FigS1F.NsrRx2_RpoE-3.png" width 600 > height 487 supersample 4 transparentBackground true > show #!16 models > hide #15 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/FigS1G.NsrRx2_RpoE-4.png" width 600 > height 487 supersample 4 transparentBackground true > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/NsrR_RpoE.cxs" > show #2 models > hide #!16 models > show #!12 models > hide #2 models > show #2 models > hide #!12 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/FigS1A.NsrR_RpoE.png" width 600 > height 487 supersample 4 transparentBackground true > ui tool show "Color Actions" > show #17 models > hide #2 models > show #!8 models > hide #17 models > save "/Users/taic/OneDrive - National Institutes of > Health/MacBookPro021/project/KarlT/AF3/NsrRx2_RpoE.cxs" > close session > open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_0.cif Chain information for fold_nucleosome_tf_model_0.cif #1 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_1.cif Chain information for fold_nucleosome_tf_model_1.cif #2 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_2.cif Chain information for fold_nucleosome_tf_model_2.cif #3 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_3.cif Chain information for fold_nucleosome_tf_model_3.cif #4 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_4.cif Chain information for fold_nucleosome_tf_model_4.cif #5 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . > show cartoons Computing secondary structure > hide atoms > open 8VG1 fromDatabase pdb format mmcif Summary of feedback from opening 8VG1 fetched from pdb --- note | Fetching compressed mmCIF 8vg1 from http://files.rcsb.org/download/8vg1.cif 8vg1 title: Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome [more info...] Chain information for 8vg1 #6 --- Chain | Description | UniProt A E | Histone H3.1 | H31_HUMAN 0-135 B F | Histone H4 | H4_HUMAN 0-102 C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125 I | DNA (171-MER) | J | DNA (171-MER) | O | Hepatocyte nuclear factor 3-alpha | FOXA1_HUMAN 1-472 T | Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 | MALE_ECOLI -378--13, GATA4_HUMAN 1-442 Non-standard residues in 8vg1 #6 --- ZN — zinc ion > ui tool show Matchmaker > matchmaker #1-5 to #6 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_0.cif, chain F (#1), sequence alignment score = 3127.7 RMSD between 43 pruned atom pairs is 0.620 angstroms; (across all 53 pairs: 8.007) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_1.cif, chain F (#2), sequence alignment score = 3139.7 RMSD between 43 pruned atom pairs is 0.499 angstroms; (across all 53 pairs: 7.604) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_2.cif, chain F (#3), sequence alignment score = 3142.7 RMSD between 45 pruned atom pairs is 0.524 angstroms; (across all 53 pairs: 7.070) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_3.cif, chain F (#4), sequence alignment score = 3127.7 RMSD between 44 pruned atom pairs is 0.550 angstroms; (across all 53 pairs: 6.895) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_4.cif, chain F (#5), sequence alignment score = 3115.7 RMSD between 44 pruned atom pairs is 0.584 angstroms; (across all 53 pairs: 6.506) > show cartoons > hide atoms > hide #5 models > hide #4 models > hide #3 models > hide #2 models > hide #1 models > show #1 models > hide #!6 models > color #1 bychain > show #!6 models > hide #1 models > show #1 models > hide #!6 models > show #2 models > hide #1 models > show #3 models > hide #2 models > show #4 models > hide #3 models > show #5 models > hide #4 models > show #1 models > show #!6 models > hide #5 models > hide #1 models > color #!6 bychain > show #1 models > hide #!6 models > color #1 bychain > show #!6 models > hide #1 models > select /A 6204 atoms, 6286 bonds, 777 residues, 6 models selected > show #1 models > show #2 models > show #3 models > show #4 models > show #5 models > hide #2 models > hide #3 models > hide #4 models > hide #5 models > hide #!6 models > select /E 18309 atoms, 18831 bonds, 2487 residues, 6 models selected > ui tool show Matchmaker > matchmaker #2-5#!6 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with fold_nucleosome_tf_model_1.cif, chain E (#2), sequence alignment score = 2368.2 RMSD between 6 pruned atom pairs is 1.361 angstroms; (across all 478 pairs: 29.439) Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with fold_nucleosome_tf_model_2.cif, chain E (#3), sequence alignment score = 2247 RMSD between 91 pruned atom pairs is 0.595 angstroms; (across all 478 pairs: 24.901) Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with fold_nucleosome_tf_model_3.cif, chain E (#4), sequence alignment score = 2331.6 RMSD between 11 pruned atom pairs is 1.309 angstroms; (across all 478 pairs: 27.521) Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with fold_nucleosome_tf_model_4.cif, chain E (#5), sequence alignment score = 2385 RMSD between 9 pruned atom pairs is 1.233 angstroms; (across all 478 pairs: 25.503) Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with 8vg1, chain O (#6), sequence alignment score = 1924.2 RMSD between 82 pruned atom pairs is 0.853 angstroms; (across all 102 pairs: 2.172) > show #2 models > hide #1 models > show #1 models > show #3 models > hide #1 models > show #1 models > hide #2 models > show #4 models > hide #3 models > show #5 models > hide #4 models > hide #1 models > show #1 models > hide #5 models > color sel & #1 bychain > show #2 models > hide #1 models > color sel & #2 bychain > select clear > show #3 models > hide #2 models > color #3 bychain > show #2 models > hide #3 models > select clear > color #2 bychain > show #4 models > hide #2 models > select clear > color #4 bychain > show #5 models > hide #4 models > color #5 bychain > show #!6 models > hide #5 models > select clear > color #!6 bychain > show #1 models > hide #!6 models > select /A 6204 atoms, 6286 bonds, 777 residues, 6 models selected > show #2 models > hide #1 models > show #!6 models > hide #2 models > show #1 models > hide #!6 models > show #2 models > hide #1 models > show #1 models > hide #2 models > show #!6 models > hide #1 models > select /B 4662 atoms, 4709 bonds, 598 residues, 6 models selected > color sel medium purple target acs > select clear > show #1 models > hide #!6 models > select /B 4662 atoms, 4709 bonds, 598 residues, 6 models selected > select /A 6204 atoms, 6286 bonds, 777 residues, 6 models selected > select clear > color #1 bychain > select clear > select /A 6204 atoms, 6286 bonds, 777 residues, 6 models selected > select /A 6204 atoms, 6286 bonds, 777 residues, 6 models selected > color sel medium slate blue target acs > select /B 4662 atoms, 4709 bonds, 598 residues, 6 models selected > color sel cornflower blue target acs > select /C 5820 atoms, 5890 bonds, 759 residues, 6 models selected > color sel olive target acs > color sel dark khaki target acs > select /D 5630 atoms, 5716 bonds, 725 residues, 6 models selected > color sel goldenrod target acs > select /E 18309 atoms, 18831 bonds, 2487 residues, 6 models selected > color sel coral target acs > select /F 31577 atoms, 32394 bonds, 4258 residues, 6 models selected > color sel plum target acs > select clear > select /G 19955 atoms, 22262 bonds, 1046 residues, 6 models selected > color sel light gray target acs > color sel gray target acs > select /H 19830 atoms, 22186 bonds, 1025 residues, 6 models selected > color sel tan target acs > color sel light blue target acs > select clear > show #2 models > hide #1 models > select /C 5820 atoms, 5890 bonds, 759 residues, 6 models selected > color sel olive drab target acs > color sel dark sea green target acs > select clear > select /C 5820 atoms, 5890 bonds, 759 residues, 6 models selected > color sel light green target acs > select clear > show #!6 models > hide #2 models > select /B 4662 atoms, 4709 bonds, 598 residues, 6 models selected > select #6/B 662 atoms, 669 bonds, 83 residues, 1 model selected > ui tool show "Color Actions" > color sel medium slate blue target acs > select #6/C 840 atoms, 850 bonds, 109 residues, 1 model selected > color sel cornflower blue target acs > select #6/A 799 atoms, 811 bonds, 97 residues, 1 model selected > color sel light green target acs > select #6/D 745 atoms, 756 bonds, 95 residues, 1 model selected > color sel goldenrod target acs > select #6/K Nothing selected > color coral target acs > select #6/B 662 atoms, 669 bonds, 83 residues, 1 model selected > show #1 models > show #2 models > show #3 models > show #4 models > show #5 models > select clear > color bychain > ui tool show Matchmaker > matchmaker #1-5 to #6 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_0.cif, chain F (#1), sequence alignment score = 3127.7 RMSD between 43 pruned atom pairs is 0.620 angstroms; (across all 53 pairs: 8.007) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_1.cif, chain F (#2), sequence alignment score = 3139.7 RMSD between 43 pruned atom pairs is 0.499 angstroms; (across all 53 pairs: 7.604) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_2.cif, chain F (#3), sequence alignment score = 3142.7 RMSD between 45 pruned atom pairs is 0.524 angstroms; (across all 53 pairs: 7.070) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_3.cif, chain F (#4), sequence alignment score = 3127.7 RMSD between 44 pruned atom pairs is 0.550 angstroms; (across all 53 pairs: 6.895) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_4.cif, chain F (#5), sequence alignment score = 3115.7 RMSD between 44 pruned atom pairs is 0.584 angstroms; (across all 53 pairs: 6.506) > matchmaker #1-5 to #6 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_0.cif, chain F (#1), sequence alignment score = 3127.7 RMSD between 43 pruned atom pairs is 0.620 angstroms; (across all 53 pairs: 8.007) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_1.cif, chain F (#2), sequence alignment score = 3139.7 RMSD between 43 pruned atom pairs is 0.499 angstroms; (across all 53 pairs: 7.604) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_2.cif, chain F (#3), sequence alignment score = 3142.7 RMSD between 45 pruned atom pairs is 0.524 angstroms; (across all 53 pairs: 7.070) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_3.cif, chain F (#4), sequence alignment score = 3127.7 RMSD between 44 pruned atom pairs is 0.550 angstroms; (across all 53 pairs: 6.895) Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_4.cif, chain F (#5), sequence alignment score = 3115.7 RMSD between 44 pruned atom pairs is 0.584 angstroms; (across all 53 pairs: 6.506) > hide #1 models > hide #2 models > hide #3 models > hide #4 models > hide #5 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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: MacBookPro18,3 Model Number: Z15H00105LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 42 days, 7 hours, 5 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: 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: Yes 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
Change History (2)
comment:1 by , 5 months ago
Component: | Unassigned → Window Toolkit |
---|---|
Description: | modified (diff) |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 months ago
Resolution: | → duplicate |
---|---|
Status: | assigned → closed |
This is a known crash and the ChimeraX Bug Report panel described what we know about it:
"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."
The current ChimeraX release candidate uses a newer Qt version and we have not seen these Mac multi-display crashes using it, so give that a try.
Reported by Emily Tai