id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14442 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.5-arm64-arm-64bit ChimeraX Version: 1.7.dev202309272145 (2023-09-27 21:45:56 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000002b5713000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b4707000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b36fb000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b26ef000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b16e3000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b06d7000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002af6cb000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ae6bf000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ad6b3000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ac6a7000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ab69b000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002aa68f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a8283000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001e7f22080 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py"", line 512 in cast File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py"", line 282 in data_as File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 322 in pointer File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 197 in get_prop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1876 in _update_graphics_if_needed File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 138 in invoke File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 237 in _activate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 206 in activate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 382 in activate_trigger File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 283 in check_for_drawing_change File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 65 in draw_new_frame File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 912 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1063 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, 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Bytes before following region: 105554055790423\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600038000000-600040000000 [128.0M] rw-\/rwx SM=PRV "", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":4266}, ""vmregioninfo"" : ""0xa9 is not in any region. 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""rollouts"" : [ { ""rolloutId"" : ""6391cacc75b0720ff1f8c695"", ""factorPackIds"" : { ""COREOS_ICD"" : ""63957f508061fa721c8edc4a"" }, ""deploymentId"" : 240000007 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7.dev202309272145 (2023-09-27) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/svearikeoeverdieck/Documents/sanders_lab/HIV/mAbs/V1V2/germline/7t73_PCT64.LMCA_ApexGT2.2MUT_EM.cif > format mmcif 7t73_PCT64.LMCA_ApexGT2.2MUT_EM.cif title: HIV-1 Envelope ApexGT2.2MUT in complex with PCT64.LMCA Fab [more info...] Chain information for 7t73_PCT64.LMCA_ApexGT2.2MUT_EM.cif #1 --- Chain | Description A C E | HIV Envelope ApexGT2.2MUT gp120 B D F | HIV Envelope ApexGT2.2MUT gp41 H | PCT64.LMCA Fab Heavy Chain L | PCT64.LMCA Fab Light Chain Non-standard residues in 7t73_PCT64.LMCA_ApexGT2.2MUT_EM.cif #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > style stick Changed 16010 atom styles > show cartoons > hide atoms > ui tool show ""Show Sequence Viewer"" > sequence chain /A /C /E Alignment identifier is 1 > select /A,C,E:49 27 atoms, 24 bonds, 3 residues, 1 model selected > select /A,C,E:49 27 atoms, 24 bonds, 3 residues, 1 model selected > show sel atoms > select sel @ show sel atoms > select clear > select /C:99 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select /A,C,E:116 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A,C,E:116 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > select sel @ select subtract /E:111 160 atoms, 139 bonds, 33 residues, 1 model selected > select subtract /E:112 156 atoms, 137 bonds, 32 residues, 1 model selected > select subtract /E:113 154 atoms, 135 bonds, 31 residues, 1 model selected > select subtract /E:115 148 atoms, 128 bonds, 30 residues, 1 model selected > select subtract /E:118 143 atoms, 122 bonds, 29 residues, 1 model selected > select subtract /E:117 137 atoms, 116 bonds, 28 residues, 1 model selected > select subtract /A:117 131 atoms, 109 bonds, 27 residues, 1 model selected > select subtract /A:115 125 atoms, 102 bonds, 26 residues, 1 model selected > select add /A:115 131 atoms, 107 bonds, 27 residues, 1 model selected > select subtract /A:115 125 atoms, 102 bonds, 26 residues, 1 model selected > select add /A:446 132 atoms, 108 bonds, 27 residues, 1 model selected > select subtract /A:114 128 atoms, 104 bonds, 26 residues, 1 model selected > select subtract /A:113 123 atoms, 100 bonds, 25 residues, 1 model selected > select subtract /A:112 116 atoms, 95 bonds, 24 residues, 1 model selected > select subtract /A:446 109 atoms, 89 bonds, 23 residues, 1 model selected > select /E:116 8 atoms, 7 bonds, 1 residue, 1 model selected > select sel @ select subtract /E:119 48 atoms, 39 bonds, 12 residues, 1 model selected > select subtract /E:118 43 atoms, 34 bonds, 11 residues, 1 model selected > select add /A:207 52 atoms, 42 bonds, 12 residues, 1 model selected > select subtract /A:207 43 atoms, 34 bonds, 11 residues, 1 model selected > select add /E:119 49 atoms, 39 bonds, 12 residues, 1 model selected > select add /E:118 56 atoms, 46 bonds, 13 residues, 1 model selected > select subtract /E:115 50 atoms, 39 bonds, 12 residues, 1 model selected > select subtract /E:114 46 atoms, 35 bonds, 11 residues, 1 model selected > select subtract /E:112 42 atoms, 33 bonds, 10 residues, 1 model selected > select subtract /E:113 40 atoms, 32 bonds, 9 residues, 1 model selected > select subtract /E:111 39 atoms, 32 bonds, 8 residues, 1 model selected > show sel atoms > select /E:434 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /E:202 15 atoms, 13 bonds, 2 residues, 1 model selected > select add /E:119 21 atoms, 18 bonds, 3 residues, 1 model selected > show sel atoms > select /E:203@CD 1 atom, 1 residue, 1 model selected > select /E:203 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /E:116 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select /E:210 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select /E:203 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select /E:116 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > select /E:121 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /E:121@NZ 1 atom, 1 residue, 1 model selected > select sel @ select > /A,C,E:35-40,45-47,53-56,75-76,84-87,91-92,130-133,154-162,169-177,181-183,191-193,201-202,216-218,223-228,238-239,242-245,259-261,271-274,283-312,315-323,329-334,359-361,374-378,381-385,393-395,413-421,423-424,433-435,441-456,466-470,486-491,494-499 4386 atoms, 4422 bonds, 540 residues, 1 model selected > select clear > select /E:123 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select sel @ select /A:313 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select /A,C,E:128 21 atoms, 18 bonds, 3 residues, 1 model selected > select /A,C,E:128 21 atoms, 18 bonds, 3 residues, 1 model selected > show sel atoms > select sel @ select subtract /A:168 141 atoms, 110 bonds, 41 residues, 1 model selected > select /A:168 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /A:167 17 atoms, 15 bonds, 2 residues, 1 model selected > select add /A:165 25 atoms, 22 bonds, 3 residues, 1 model selected > show sel atoms > select > /A,C,E:35-40,45-47,53-56,75-76,84-87,91-92,130-133,154-162,169-177,181-183,191-193,201-202,216-218,223-228,238-239,242-245,259-261,271-274,283-312,315-323,329-334,359-361,374-378,381-385,393-395,413-421,423-424,433-435,441-456,466-470,486-491,494-499 4386 atoms, 4422 bonds, 540 residues, 1 model selected > select /A,C,E:130 27 atoms, 24 bonds, 3 residues, 1 model selected > select /A,C,E:130 27 atoms, 24 bonds, 3 residues, 1 model selected > open 8e1p Summary of feedback from opening 8e1p fetched from pdb --- note | Fetching compressed mmCIF 8e1p from http://files.rcsb.org/download/8e1p.cif 8e1p title: Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs [more info...] Chain information for 8e1p #2 --- Chain | Description | UniProt A C J | PGT124 Fab Light Chain | B D K | PGT124 Fab Heavy Chain | E G M | BG505-SOSIP.v4.1-GT1.2gp120 | F H N | germline PGV20 heavy chain | I | germline PGV20 light chain | L O | germline PGV20 light chain | X Y Z | Envelope glycoprotein gp41 | Q2N0S6_9HIV1 512-664 Non-standard residues in 8e1p #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide #!1 models > select add #1 16010 atoms, 16436 bonds, 9 pseudobonds, 1985 residues, 2 models selected > select subtract #1 Nothing selected > select add #2 34410 atoms, 35327 bonds, 22 pseudobonds, 4405 residues, 2 models selected > show sel cartoons > style sel stick Changed 34410 atom styles > show sel cartoons > hide sel atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/C #1/E Alignment identifier is 1 > select clear > select #1/A,C,E:476 33 atoms, 30 bonds, 3 residues, 1 model selected > select #1/A,C,E:476 33 atoms, 30 bonds, 3 residues, 1 model selected > select #2/G:475 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/G:476 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select sel @ ui tool show ""Show Sequence Viewer"" > sequence chain #2/F #2/H #2/N Alignment identifier is 2 > select #2/G:476 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel cyan > ui tool show Rotamers > swapaa interactive sel ARG rotLib Richardson.common 8e1p #2/G ARG 476: phi -65.1, psi -22.9 trans Changed 272 bond radii > select #1/A,C,E:469 33 atoms, 30 bonds, 3 residues, 1 model selected > select #1/A,C,E:469 33 atoms, 30 bonds, 3 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/E #2/G #2/M Alignment identifier is 1 > select #2/E,G,M:469 33 atoms, 30 bonds, 3 residues, 1 model selected > select #2/E,G,M:469 33 atoms, 30 bonds, 3 residues, 1 model selected > open 7t76 7t76 title: HIV-1 Envelope ApexGT3 in complex with PG9.iGL Fab [more info...] Chain information for 7t76 #3 --- Chain | Description A C E | HIV Envelope ApexGT3 gp120 B D F | HIV Envelope ApexGT3 gp41 H | PG9.iGL Fab Heavy Chain L | PG9.iGL Fab Light Chain Non-standard residues in 7t76 #3 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide #!2 models > show #!3 cartoons > hide #!3 atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A #3/C #3/E Alignment identifier is 1 > select #3/A,C,E:150 24 atoms, 21 bonds, 3 residues, 1 model selected > select #3/A,C,E:150 24 atoms, 21 bonds, 3 residues, 1 model selected > select #3/C:161 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/E:168 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > select #3/H:100F 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 52 atoms, 54 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 52 atom styles > select #3/E:168 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel GLU rotLib Richardson.common 7t76 #3/E LYS 168: phi -106.4, psi 140.2 trans Changed 48 bond radii > swapaa #!3/E:168 GLU criteria 3 rotLib Richardson.common Using Richardson.common library 7t76 #!3/E LYS 168: phi -106.4, psi 140.2 trans Applying GLU rotamer (chi angles: -65.0 -65.0 -40.0) to 7t76 #!3/E GLU 168 > select #3/A,C,E:172 33 atoms, 30 bonds, 3 residues, 1 model selected > select #3/A,C,E:172 33 atoms, 30 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 33 atom styles > select #3/A,C,E:164 27 atoms, 24 bonds, 3 residues, 1 model selected > select #3/A,C,E:164 27 atoms, 24 bonds, 3 residues, 1 model selected > close #2 > close #3 > show #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain /A /C /E Alignment identifier is 1 > select /A,C,E:159 33 atoms, 33 bonds, 3 residues, 1 model selected > select /A,C,E:159 33 atoms, 33 bonds, 3 residues, 1 model selected > select /A,C,E:176 33 atoms, 33 bonds, 3 residues, 1 model selected > select /A,C,E:176 33 atoms, 33 bonds, 3 residues, 1 model selected > show sel atoms > select /H:100F 8 atoms, 7 bonds, 1 residue, 1 model selected > select subtract /H:100F Nothing selected > select /H:100F 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 82 atoms, 86 bonds, 8 residues, 1 model selected > show sel atoms > select /A:167 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /E:128@CB 9 atoms, 7 bonds, 2 residues, 1 model selected > select subtract /E:128 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /E:128 15 atoms, 13 bonds, 2 residues, 1 model selected > select add /H:100G 23 atoms, 20 bonds, 3 residues, 1 model selected > color sel byhetero > ui tool show Distances > select /A:167@ND2 1 atom, 1 residue, 1 model selected > select add /H:100G@OD2 2 atoms, 2 residues, 1 model selected > distance /A:167@ND2 /H:100G@OD2 Distance between /A ASN 167 ND2 and /H ASP 100G OD2: 3.302Å > select /A:167@OD1 1 atom, 1 residue, 1 model selected > select add /E:128@OG1 2 atoms, 2 residues, 1 model selected > distance /A:167@OD1 /E:128@OG1 Distance between /A ASN 167 OD1 and /E THR 128 OG1: 3.364Å > select /A:167 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ASP rotLib Richardson.common /A ASN 167: phi -86.6, psi 2.0 trans Changed 25 bond radii > select /A:169 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7.dev202309272145 (2023-09-27) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: Z17G002THN/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8422.141.2 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.5 (22G74) Kernel Version: Darwin 22.6.0 Time since boot: 27 days, 5 hours, 30 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 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 HP E24i G4: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.0 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.11.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.48 ChimeraX-AtomicLibrary: 10.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.3 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202309272145 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.11 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.10 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.32.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 contourpy: 1.1.1 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.42.1 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.2 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.2 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.5 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX